
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/KIRP-TP/4467466/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRP-TP/4434786/KIRP-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRP-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=KIRP-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRP-TP/4434786/KIRP-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/4467466/transformed.cor.cli.txt"

nPatients in clinical file=129, in cluster file=158, common to both=129
[1] "Reduce the number of clustering variables from 80 to 63."
[1]  63 129
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               11               118 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               11               118 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21               108 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               21               108 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               23               106 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               23               106 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               36                93 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               36                93 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               41                88 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               41                88 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               123 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               123 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               124 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               124 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               109 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               109 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               110 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               19               110 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4               125 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4               125 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3               126 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3               126 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               71                58 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               71                58 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               73                56 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               73                56 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10               119 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10               119 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13               116 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13               116 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                124 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                124 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                125 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                125 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                123 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                123 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                125 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                125 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                 80 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                49                 80 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                49                 80 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                49                 80 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                114 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                15                114 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                66                 63 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                66                 63 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                64                 65 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                64                 65 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                71                 58 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                71                 58 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                84                 45 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                84                 45 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                122 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                122 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                124 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                124 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                42                 87 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                42                 87 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                45                 84 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                45                 84 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                123 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 6                123 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               38                91 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               38                91 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               17               112 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               17               112 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               119 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               119 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               120 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9               120 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               126 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               126 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11               118 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11               118 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               12               117 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               12               117 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6               123 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6               123 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5               124 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5               124 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10               119 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               10               119 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12               117 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12               117 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5               124 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5               124 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               126 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               126 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               17               112 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               17               112 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               18               111 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               18               111 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                121 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                121 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                121 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                121 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                120 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                120 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                12                117 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                12                117 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                11                118 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                11                118 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                27                102 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                27                102 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                14                115 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                14                115 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                125 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                125 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                125 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                125 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                122 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                122 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                20                109 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                20                109 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                21                108 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                21                108 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 9                120 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 9                120 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                121 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                121 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                23                106 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                23                106 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                 98 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                 98 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               19               110 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               19               110 
[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] "KARNOFSKYPERFORMANCESCORE"             
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "BATCHNUMBER"                           

Input Data has 19 rows and 129 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
           1           21          485            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
           1           27           NA            7           49          140 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
           1            2           21           22            1            3 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3467 
          NA            1           NA           NA           NA         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
        1636          412          922          763         1357          595 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         223          498          307          347          334          147 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          856          803          626           14           33 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
         460          196           36           64          207            5 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        2638          585           NA         1938           NA           NA 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1454           NA         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         771          403           NA          232           29          364 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
          NA           84         3759           NA         2948         2839 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
          NA         1864         1532         1516          799          612 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
          NA          232          213          217          115          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          418 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92          876         2428         2459 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
          NA         1856         1669         1040          578          757 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
         208         1574         1479           NA         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         765          445          428         5924           NA          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-7128 TCGA-HE-7129 
         235           32          178           91           NA           NA 
TCGA-HE-7130 TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
          NA          139          430           62           33          123 
TCGA-J7-6720 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
          NA          112          173 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=96,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	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=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=16,	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] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
[9] "YEAROFTOBACCOSMOKINGONSET"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 129 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
74 16 38  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   74    16    39 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
74 16 38  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   74    16    39 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
26 12  4 
[1] "table(vv)"
vv
N0 N1 N2 
26 12  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
26 12  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
26 12  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=4, binary=FALSE, numeric=TRUE
YEAROFTOBACCOSMOKINGONSET, nv=3, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1Q GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    7  3
  1Q GAIN WILD-TYPE 97 12
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               10               109 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                12 
$`1Q GAIN MUTATED`
TCGA-A4-7287 TCGA-AL-3466 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
        0.69         9.63        30.28        25.35         7.63         0.95 
TCGA-BQ-5893 TCGA-G7-6789 TCGA-GL-7966 TCGA-IA-A40Y 
        7.89         4.01         3.68         2.04 

$`1Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3468 
        0.72         0.03         0.10         0.03        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        19.56         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       16.37        10.09        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.14        26.40        20.58         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
        6.44         1.18         2.10         6.81         0.16        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       21.63        40.83        26.04        26.04        13.25        10.88 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         2.76       123.58        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.37        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.00         7.13         3.78        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        28.80        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        34.19        19.00        24.89 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.75        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.63        14.07       194.76         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
        2.99         4.57        14.14         1.08         4.04         3.68 
TCGA-PJ-A5Z9 
        5.69 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.69              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            30.28            194.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             5.82             14.63 
[1] "0.7 - 30.3 (5.8)"   "0.0 - 194.8 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
[1] "hr=" "12" 
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         1        0         7        3
  1Q GAIN WILD-TYPE      68       10        23        7
D1V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 1                68
  STAGE II                0                10
  STAGE III               7                23
  STAGE IV                3                 7
                   vv
clus                T1 T2 T3+T4
  1Q GAIN MUTATED    1  0    10
  1Q GAIN WILD-TYPE 73 16    29
D1V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  1                73
  T2                  0                16
  T3+T4              10                29
                   vv
clus                N0 N1 N2
  1Q GAIN MUTATED    4  4  1
  1Q GAIN WILD-TYPE 22  8  3
D1V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0               4                22
  N1               4                 8
  N2               1                 3
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED    5  2  4
  1Q GAIN WILD-TYPE 52  4 53
D1V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               5                52
  M1               2                 4
  MX               4                53
D1V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    6  5
  1Q GAIN WILD-TYPE 34 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    5
  1Q GAIN WILD-TYPE   34   84
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               6                34
  MALE                 5                84
D1V8, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-5561 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-7502 
"1Q GAIN WILD-TYPE" 
D1V9, continuous
D1V10, continuous

Clustering(2) Variable = 2P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   15  4
  2P GAIN WILD-TYPE 89 11
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               19               100 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                11 
$`2P GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3471 TCGA-B1-7332 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 
        9.63        13.55         7.33         0.46         2.10        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 TCGA-G7-6789 
        7.89         2.76        96.92        13.61        51.16         4.01 
TCGA-G7-6790 TCGA-G7-6795 TCGA-GL-7966 TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40Y 
       51.75        39.25         3.68         2.99         4.57         2.04 
TCGA-PJ-A5Z9 
        5.69 

$`2P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       53.79        30.31        25.08        44.61        19.56        16.37 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.58         1.08        15.12         6.44         1.18 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.81         0.16        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        0.95       123.58        48.26        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.37        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
        7.00         7.13         3.78        11.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       28.80        79.82        80.84        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
       19.00        24.89        48.62        11.05        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.63        14.07       194.76         7.73         1.05         5.85 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
       14.14         1.08         4.04         3.68 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.46              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            96.92            194.76 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            7.330            15.535 
[1] "0.5 - 96.9 (7.3)"   "0.0 - 194.8 (15.5)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
[1] "hr=" "2.6"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        10        1         4        5
  2P GAIN WILD-TYPE      59        9        26        5
D2V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                10                59
  STAGE II                1                 9
  STAGE III               4                26
  STAGE IV                5                 5
                   vv
clus                T1 T2 T3+T4
  2P GAIN MUTATED   10  3     8
  2P GAIN WILD-TYPE 64 13    31
D2V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                 10                64
  T2                  3                13
  T3+T4               8                31
                   vv
clus                N0 N1 N2
  2P GAIN MUTATED    4  5  1
  2P GAIN WILD-TYPE 22  7  3
D2V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               4                22
  N1               5                 7
  N2               1                 3
                   vv
clus                M0 M1 MX
  2P GAIN MUTATED    4  4 11
  2P GAIN WILD-TYPE 53  2 46
D2V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               4                53
  M1               4                 2
  MX              11                46
D2V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    8 13
  2P GAIN WILD-TYPE 32 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8   13
  2P GAIN WILD-TYPE   32   76
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               8                32
  MALE                13                76
D2V8, continuous
D2V9, continuous
D2V10, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"        "2P GAIN WILD-TYPE"     
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                 1 
named character(0)

Clustering(3) Variable = 2Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   17  4
  2Q GAIN WILD-TYPE 87 11
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21                98 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4                11 
$`2Q GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-7173 TCGA-B1-7332 TCGA-B9-4117 TCGA-B9-A44B 
        9.63        13.55        44.61         7.33         0.46         2.10 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 
       11.97         7.89         2.76        96.92        13.61        51.16 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-GL-7966 TCGA-GL-A59T 
        4.01        51.75        39.25        14.07         3.68         2.99 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-PJ-A5Z9 
        4.57         2.04         5.69 

$`2Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       53.79        30.31        25.08        19.56        16.37        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       11.41        10.98         4.83        50.50        28.14        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.58         1.08        15.12         6.44         1.18         6.81 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        0.16        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.63         0.95 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.58        48.26        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.13         3.78        11.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.82        80.84        61.02        54.87        34.19        19.00 
TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       24.89        48.62        11.05        34.82        25.15        14.63 
TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-IA-A40X TCGA-IZ-8195 
      194.76         7.73         1.05         5.85        14.14         1.08 
TCGA-IZ-8196 TCGA-PJ-A5Z8 
        4.04         3.68 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            96.92            194.76 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            7.890            15.535 
[1] "0.5 - 96.9 (7.9)"   "0.0 - 194.8 (15.5)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
[1] "hr=" "2.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        11        1         4        6
  2Q GAIN WILD-TYPE      58        9        26        4
D3V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                11                58
  STAGE II                1                 9
  STAGE III               4                26
  STAGE IV                6                 4
                   vv
clus                T1 T2 T3+T4
  2Q GAIN MUTATED   11  3     9
  2Q GAIN WILD-TYPE 63 13    30
D3V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                 11                63
  T2                  3                13
  T3+T4               9                30
                   vv
clus                N0 N1 N2
  2Q GAIN MUTATED    4  5  2
  2Q GAIN WILD-TYPE 22  7  2
D3V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0               4                22
  N1               5                 7
  N2               2                 2
                   vv
clus                M0 M1 MX
  2Q GAIN MUTATED    5  4 12
  2Q GAIN WILD-TYPE 52  2 45
D3V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               5                52
  M1               4                 2
  MX              12                45
D3V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    9 14
  2Q GAIN WILD-TYPE 31 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9   14
  2Q GAIN WILD-TYPE   31   75
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               9                31
  MALE                14                75
D3V8, continuous
D3V9, continuous
D3V10, continuous
[1] "Remove cluster labels:" "2Q GAIN MUTATED"        "2Q GAIN WILD-TYPE"     
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                 1 
named character(0)

Clustering(4) Variable = 3P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   29  2
  3P GAIN WILD-TYPE 75 13
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               31                88 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                13 
$`3P GAIN MUTATED`
TCGA-A4-7287 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3468 
        0.69         0.07         0.72         0.10         0.03        53.79 
TCGA-AL-3471 TCGA-B1-7332 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
       13.55         7.33        11.41        28.14         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-7045 
       15.12         6.44         1.18        47.80        26.04        48.26 
TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7837 
       96.92         7.00         3.78        11.61        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6133 TCGA-G7-6790 TCGA-GL-6846 TCGA-GL-A59T 
       24.46        28.80        51.16        51.75       194.76         2.99 
TCGA-PJ-A5Z9 
        5.69 

$`3P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8517 
        0.23         1.61         4.60         0.03         0.69         0.03 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
        9.63        58.45        30.31        25.08        44.61        19.56 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 
       16.37        10.09        10.98         4.83        50.50        26.40 
TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 
       20.58         2.10         6.81         0.16        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.84        63.72        22.92        43.17        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
        0.95        11.97         7.89         2.76       123.58        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.37        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 
       11.28         7.63         7.13        13.61       129.86        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
        3.75        14.63         3.02        79.82        80.84        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6792 
       54.87        34.19        19.00        24.89         4.01        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        14.63        14.07 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-IA-A40U TCGA-IA-A40X 
        3.68         7.73         1.05         5.85         4.57        14.14 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
        2.04         1.08         4.04         3.68 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.03              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           194.76            129.86 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           11.610            14.105 
[1] "0.0 - 194.8 (11.6)" "0.0 - 129.9 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
[1] "hr=" "2.4"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED        24        3         4        1
  3P GAIN WILD-TYPE      45        7        26        9
D4V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                24                45
  STAGE II                3                 7
  STAGE III               4                26
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  3P GAIN MUTATED   25  6     5
  3P GAIN WILD-TYPE 49 10    34
D4V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                 25                49
  T2                  6                10
  T3+T4               5                34
                   vv
clus                N0 N1 N2
  3P GAIN MUTATED    3  1  0
  3P GAIN WILD-TYPE 23 11  4
D4V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               3                23
  N1               1                11
  N2               0                 4
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED   14  0 18
  3P GAIN WILD-TYPE 43  6 39
D4V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              14                43
  M1               0                 6
  MX              18                39
D4V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    9 27
  3P GAIN WILD-TYPE 31 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9   27
  3P GAIN WILD-TYPE   31   62
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               9                31
  MALE                27                62
D4V8, continuous
D4V9, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"        "3P GAIN WILD-TYPE"     
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 2 
named character(0)
D4V10, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"        "3P GAIN WILD-TYPE"     
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 2 
named character(0)

Clustering(5) Variable = 3Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   34  2
  3Q GAIN WILD-TYPE 70 13
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               36                83 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                13 
$`3Q GAIN MUTATED`
TCGA-A4-7287 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-A48D 
        0.69         0.07         0.69         0.72         0.10         0.03 
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-7332 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 
       53.79        13.55         7.33        11.41        28.14         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-BQ-5881 
        1.08        15.12         6.44         1.18         2.10        47.80 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 
       26.04         7.63        48.26        96.92         7.00         3.78 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
       35.93        37.55        24.46        28.80        80.84        51.16 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-G7-6790 TCGA-GL-6846 TCGA-GL-A59T TCGA-PJ-A5Z9 
       54.87        34.19        51.75       194.76         2.99         5.69 

$`3Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 TCGA-AL-3466 
        0.23         1.61         4.60         0.03         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       58.45        30.31        25.08        44.61        19.56        16.37 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
       10.09        10.98         4.83        50.50        26.40        20.58 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.81         0.16        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.17        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25        10.88         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.58        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 
       49.84        26.27        20.12        11.28         7.63         7.13 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       11.61        13.61       129.86        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
        3.02        79.82        61.02        19.00        24.89         4.01 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        14.63 
TCGA-G7-7502 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-IA-A40U 
       14.07         3.68         7.73         1.05         5.85         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
       14.14         2.04         1.08         4.04         3.68 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.03              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           194.76            129.86 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.48             14.07 
[1] "0.0 - 194.8 (12.5)" "0.0 - 129.9 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
[1] "hr=" "3.2"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        27        3         6        1
  3Q GAIN WILD-TYPE      42        7        24        9
D5V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                27                42
  STAGE II                3                 7
  STAGE III               6                24
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  3Q GAIN MUTATED   28  6     7
  3Q GAIN WILD-TYPE 46 10    32
D5V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                 28                46
  T2                  6                10
  T3+T4               7                32
                   vv
clus                N0 N1 N2
  3Q GAIN MUTATED    4  1  0
  3Q GAIN WILD-TYPE 22 11  4
D5V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0               4                22
  N1               1                11
  N2               0                 4
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED   15  0 21
  3Q GAIN WILD-TYPE 42  6 36
D5V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              15                42
  M1               0                 6
  MX              21                36
D5V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    9 32
  3Q GAIN WILD-TYPE 31 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      9   32
  3Q GAIN WILD-TYPE   31   57
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               9                31
  MALE                32                57
D5V8, continuous
D5V9, continuous
[1] "Remove cluster labels:" "3Q GAIN WILD-TYPE"     
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                 1 
     TCGA-B9-A44B      TCGA-GL-A59T      TCGA-PJ-A5Z9 
"3Q GAIN MUTATED" "3Q GAIN MUTATED" "3Q GAIN MUTATED" 
D5V10, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"        "3Q GAIN WILD-TYPE"     
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 2 
named character(0)

Clustering(6) Variable = 4P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     4   2
  4P GAIN WILD-TYPE 100  13
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               113 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                13 
$`4P GAIN MUTATED`
TCGA-AL-3466 TCGA-B9-4114 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-6795 
        9.63        28.14         0.16        11.97         4.01        39.25 

$`4P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        26.40        20.58         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5876 
        6.44         1.18         2.10         6.81        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.84        63.72        22.92        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         7.63         0.95         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       34.19        19.00        24.89        51.75        48.62        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       34.82        25.15        14.63        14.07       194.76         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X 
        7.73         1.05         5.85         2.99         4.57        14.14 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        2.04         1.08         4.04         3.68         5.69 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.16              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            39.25            194.76 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            10.80             14.07 
[1] "0.2 - 39.2 (10.8)"  "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "5.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         3        0         0        2
  4P GAIN WILD-TYPE      66       10        30        8
D6V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 3                66
  STAGE II                0                10
  STAGE III               0                30
  STAGE IV                2                 8
                   vv
clus                T1 T2 T3+T4
  4P GAIN MUTATED    3  1     2
  4P GAIN WILD-TYPE 71 15    37
D6V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  3                71
  T2                  1                15
  T3+T4               2                37
                   vv
clus                N0 N1 N2
  4P GAIN MUTATED    2  1  1
  4P GAIN WILD-TYPE 24 11  3
D6V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               2                24
  N1               1                11
  N2               1                 3
                   vv
clus                M0 M1 MX
  4P GAIN MUTATED    1  1  3
  4P GAIN WILD-TYPE 56  5 54
D6V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               1                56
  M1               1                 5
  MX               3                54
D6V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    1  5
  4P GAIN WILD-TYPE 39 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    5
  4P GAIN WILD-TYPE   39   84
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                39
  MALE                 5                84
D6V8, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-5561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-7502 
"4P GAIN WILD-TYPE" 
D6V9, continuous
D6V10, continuous

Clustering(7) Variable = 4Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 100  14
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               114 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                14 
$`4Q GAIN MUTATED`
TCGA-B9-4114 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-6795 
       28.14         0.16        11.97         4.01        39.25 

$`4Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        53.79        13.55        30.31        25.08        44.61 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       19.56         7.33        16.37        10.09        11.41        10.98 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        4.83        50.50        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 
       15.12         6.44         1.18         2.10         6.81        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.88         7.63         0.95         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.37        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        28.80        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 
       54.87        34.19        19.00        24.89        51.75        48.62 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       11.05        34.82        25.15        14.63        14.07       194.76 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
        3.68         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         4.04         3.68         5.69 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.16              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            39.25            194.76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           11.970            13.905 
[1] "0.2 - 39.2 (12.0)"  "0.0 - 194.8 (13.9)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         3        0         0        1
  4Q GAIN WILD-TYPE      66       10        30        9
D7V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 3                66
  STAGE II                0                10
  STAGE III               0                30
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  4Q GAIN MUTATED    3  1     1
  4Q GAIN WILD-TYPE 71 15    38
D7V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  3                71
  T2                  1                15
  T3+T4               1                38
                   vv
clus                N0 N1 N2
  4Q GAIN MUTATED    2  0  1
  4Q GAIN WILD-TYPE 24 12  3
D7V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               2                24
  N1               0                12
  N2               1                 3
                   vv
clus                M0 M1 MX
  4Q GAIN MUTATED    1  0  3
  4Q GAIN WILD-TYPE 56  6 54
D7V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               1                56
  M1               0                 6
  MX               3                54
D7V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    1  4
  4Q GAIN WILD-TYPE 39 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    4
  4Q GAIN WILD-TYPE   39   85
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                39
  MALE                 4                85
D7V8, continuous
D7V9, continuous
D7V10, continuous

Clustering(8) Variable = 5P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   15  2
  5P GAIN WILD-TYPE 89 13
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               17               102 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                13 
$`5P GAIN MUTATED`
TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 
        4.60         0.72         0.03         9.63        25.08        19.56 
TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 
        0.46         0.16        25.35         0.95        11.97        24.46 
TCGA-DZ-6131 TCGA-EV-5902 TCGA-G7-6789 TCGA-GL-A4EM TCGA-IA-A40Y 
       79.82        19.00         4.01         1.05         2.04 

$`5P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.89         0.23         1.61         0.03         0.07         0.69 
TCGA-A4-8517 TCGA-A4-8518 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        0.03         0.10        58.45        53.79        13.55        30.31 
TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       44.61         7.33        16.37        10.09        11.41        10.98 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
        4.83        50.50        28.14        26.40        20.58         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 
       15.12         6.44         1.18         2.10         6.81        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.88         7.63         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        28.80        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 
       51.16        61.02        54.87        34.19        24.89        51.75 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
       14.07       194.76         3.68         7.73         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.57        14.14         1.08         4.04         3.68         5.69 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            79.82            194.76 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            4.600            14.385 
[1] "0.0 - 79.8 (4.6)"   "0.0 - 194.8 (14.4)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         8        1         7        3
  5P GAIN WILD-TYPE      61        9        23        7
D8V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 8                61
  STAGE II                1                 9
  STAGE III               7                23
  STAGE IV                3                 7
                   vv
clus                T1 T2 T3+T4
  5P GAIN MUTATED    8  3     9
  5P GAIN WILD-TYPE 66 13    30
D8V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                  8                66
  T2                  3                13
  T3+T4               9                30
                   vv
clus                N0 N1 N2
  5P GAIN MUTATED    7  2  1
  5P GAIN WILD-TYPE 19 10  3
D8V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0               7                19
  N1               2                10
  N2               1                 3
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED    7  2 10
  5P GAIN WILD-TYPE 50  4 47
D8V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               7                50
  M1               2                 4
  MX              10                47
D8V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    5 15
  5P GAIN WILD-TYPE 35 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5   15
  5P GAIN WILD-TYPE   35   74
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               5                35
  MALE                15                74
D8V8, continuous
D8V9, continuous
D8V10, continuous

Clustering(9) Variable = 5Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   14  2
  5Q GAIN WILD-TYPE 90 13
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               16               103 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                13 
$`5Q GAIN MUTATED`
TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 
        4.60         0.72         0.03         9.63        25.08        19.56 
TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 
        0.46         0.16        25.35         0.95        11.97        24.46 
TCGA-EV-5902 TCGA-G7-6789 TCGA-GL-A4EM TCGA-IA-A40Y 
       19.00         4.01         1.05         2.04 

$`5Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.89         0.23         1.61         0.03         0.07         0.69 
TCGA-A4-8517 TCGA-A4-8518 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        0.03         0.10        58.45        53.79        13.55        30.31 
TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       44.61         7.33        16.37        10.09        11.41        10.98 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
        4.83        50.50        28.14        26.40        20.58         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 
       15.12         6.44         1.18         2.10         6.81        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.88         7.63         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.74         3.75        14.63         3.02        28.80        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       80.84        51.16        61.02        54.87        34.19        24.89 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.75        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
       14.63        14.07       194.76         3.68         7.73         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
        2.99         4.57        14.14         1.08         4.04         3.68 
TCGA-PJ-A5Z9 
        5.69 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            25.35            194.76 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            4.305            14.630 
[1] "0.0 - 25.4 (4.3)"   "0.0 - 194.8 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "hr=" "3"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         8        1         6        3
  5Q GAIN WILD-TYPE      61        9        24        7
D9V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 8                61
  STAGE II                1                 9
  STAGE III               6                24
  STAGE IV                3                 7
                   vv
clus                T1 T2 T3+T4
  5Q GAIN MUTATED    8  3     8
  5Q GAIN WILD-TYPE 66 13    31
D9V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                  8                66
  T2                  3                13
  T3+T4               8                31
                   vv
clus                N0 N1 N2
  5Q GAIN MUTATED    6  2  1
  5Q GAIN WILD-TYPE 20 10  3
D9V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               6                20
  N1               2                10
  N2               1                 3
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED    7  2  9
  5Q GAIN WILD-TYPE 50  4 48
D9V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               7                50
  M1               2                 4
  MX               9                48
D9V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    5 14
  5Q GAIN WILD-TYPE 35 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5   14
  5Q GAIN WILD-TYPE   35   75
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               5                35
  MALE                14                75
D9V8, continuous
D9V9, continuous
D9V10, continuous

Clustering(10) Variable = 6P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     2   2
  6P GAIN WILD-TYPE 102  13
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4               115 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                13 
$`6P GAIN MUTATED`
TCGA-AL-3466 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-DW-5561 
        9.63         7.89        93.34        13.61 

$`6P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12         6.44         1.18         2.10         6.81         0.16 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.63         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76       123.58        48.26        96.92        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.37        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
        7.00         7.13         3.78        11.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       34.19        19.00        24.89         4.01        51.75        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        14.63        14.07 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.76         3.68         7.73         1.05         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
        4.57        14.14         2.04         1.08         4.04         3.68 
TCGA-PJ-A5Z9 
        5.69 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             7.89              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            93.34            194.76 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            11.62             14.07 
[1] "7.9 - 93.3 (11.6)"  "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "3.7"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         1        0         1        2
  6P GAIN WILD-TYPE      68       10        29        8
D10V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 1                68
  STAGE II                0                10
  STAGE III               1                29
  STAGE IV                2                 8
                   vv
clus                T1 T2 T3+T4
  6P GAIN MUTATED    1  0     3
  6P GAIN WILD-TYPE 73 16    36
D10V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                  1                73
  T2                  0                16
  T3+T4               3                36
                   vv
clus                N0 N1 N2
  6P GAIN MUTATED    1  2  0
  6P GAIN WILD-TYPE 25 10  4
D10V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               1                25
  N1               2                10
  N2               0                 4
                   vv
clus                M0 M1 MX
  6P GAIN MUTATED    2  2  0
  6P GAIN WILD-TYPE 55  4 57
D10V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               2                55
  M1               2                 4
  MX               0                57
D10V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    0  4
  6P GAIN WILD-TYPE 40 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    4
  6P GAIN WILD-TYPE   40   85
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               0                40
  MALE                 4                85
D10V8, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                20 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-7834 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-EV-5901 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D10V9, continuous
D10V10, continuous

Clustering(11) Variable = 6Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     1   2
  6Q GAIN WILD-TYPE 103  13
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3               116 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                13 
$`6Q GAIN MUTATED`
TCGA-AL-3466 TCGA-BQ-5893 TCGA-DW-5561 
        9.63         7.89        13.61 

$`6Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12         6.44         1.18         2.10         6.81         0.16 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.63         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 
        7.63         7.00         7.13         3.78        11.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        28.80        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       54.87        34.19        19.00        24.89         4.01        51.75 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.07       194.76         3.68         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             7.89              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.61            194.76 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            9.630            14.105 
[1] "7.9 - 13.6 (9.6)"   "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "16" 
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         1        0         0        2
  6Q GAIN WILD-TYPE      68       10        30        8
D11V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 1                68
  STAGE II                0                10
  STAGE III               0                30
  STAGE IV                2                 8
                   vv
clus                T1 T2 T3+T4
  6Q GAIN MUTATED    1  0     2
  6Q GAIN WILD-TYPE 73 16    37
D11V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                  1                73
  T2                  0                16
  T3+T4               2                37
                   vv
clus                N0 N1 N2
  6Q GAIN MUTATED    0  2  0
  6Q GAIN WILD-TYPE 26 10  4
D11V5, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                40 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846        TCGA-GL-7966 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                M0 M1 MX
  6Q GAIN MUTATED    1  2  0
  6Q GAIN WILD-TYPE 56  4 57
D11V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               1                56
  M1               2                 4
  MX               0                57
D11V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    0  3
  6Q GAIN WILD-TYPE 40 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    3
  6Q GAIN WILD-TYPE   40   86
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               0                40
  MALE                 3                86
D11V8, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                20 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-7834 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-EV-5901 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D11V9, continuous
D11V10, continuous

Clustering(12) Variable = 7P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   59  5
  7P GAIN WILD-TYPE 45 10
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               64                55 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                10 
$`7P GAIN MUTATED`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
       15.95         0.03         0.89         1.61         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        0.69         0.72         0.03        53.79        13.55        30.31 
TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       44.61        16.37        11.41         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40         0.46         1.08        15.12         6.44         1.18 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5894 
       47.80        26.04        25.35        10.88         0.95         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
      123.58        48.26        96.92        50.37         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46         3.75        14.63         3.02        28.80 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 
       80.84        51.16        61.02        34.19        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A59R 
       51.75        39.25        14.07       194.76         7.73         5.85 
TCGA-GL-A59T TCGA-IA-A40Y TCGA-IZ-8196 TCGA-PJ-A5Z9 
        2.99         2.04         4.04         5.69 

$`7P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
        0.03         0.69         0.10        35.18         0.23         4.60 
TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
        0.10         0.03         9.63        58.45        25.08        19.56 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 
        7.33        10.09        10.98        20.58         2.10         6.81 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        0.16        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       43.17        21.63        40.83        30.28        26.04        13.25 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        7.63        11.97         7.89        93.34        44.84        61.28 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-DZ-6131 
       49.84        26.27        20.12        11.28        13.74        79.82 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
       54.87        19.00        48.62        11.05        34.82        25.15 
TCGA-G7-7501 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
       14.63         3.68         1.05         4.57        14.14         1.08 
TCGA-PJ-A5Z8 
        3.68 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           194.76             93.34 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            13.58             14.14 
[1] "0.0 - 194.8 (13.6)" "0.0 - 93.3 (14.1)" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
[1] "hr=" "2.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED        46        3         9        6
  7P GAIN WILD-TYPE      23        7        21        4
D12V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                46                23
  STAGE II                3                 7
  STAGE III               9                21
  STAGE IV                6                 4
                   vv
clus                T1 T2 T3+T4
  7P GAIN MUTATED   48  9    14
  7P GAIN WILD-TYPE 26  7    25
D12V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                 48                26
  T2                  9                 7
  T3+T4              14                25
                   vv
clus                N0 N1 N2
  7P GAIN MUTATED   11  4  2
  7P GAIN WILD-TYPE 15  8  2
D12V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              11                15
  N1               4                 8
  N2               2                 2
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   26  3 36
  7P GAIN WILD-TYPE 31  3 21
D12V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              26                31
  M1               3                 3
  MX              36                21
D12V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   17 54
  7P GAIN WILD-TYPE 23 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     17   54
  7P GAIN WILD-TYPE   23   35
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              17                23
  MALE                54                35
D12V8, continuous
D12V9, continuous
[1] "Remove cluster labels:" "7P GAIN MUTATED"        "7P GAIN WILD-TYPE"     
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 2 
named character(0)
D12V10, continuous
[1] "Remove cluster labels:" "7P GAIN MUTATED"        "7P GAIN WILD-TYPE"     
clus
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 1 
named character(0)

Clustering(13) Variable = 7Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   60  5
  7Q GAIN WILD-TYPE 44 10
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               65                54 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                10 
$`7Q GAIN MUTATED`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
       15.95         0.03         0.89         1.61         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        0.69         0.72         0.03        53.79        13.55        30.31 
TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       44.61        16.37        11.41         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40         0.46         1.08        15.12         6.44         1.18 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 
       47.80        26.04        25.35        10.88         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 
        2.76       123.58        48.26        96.92        50.37         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        24.46         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 
       28.80        80.84        51.16        61.02        34.19        24.89 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 
        4.01        51.75        39.25        14.07       194.76         7.73 
TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40Y TCGA-IZ-8196 TCGA-PJ-A5Z9 
        5.85         2.99         2.04         4.04         5.69 

$`7Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
        0.03         0.69         0.10        35.18         0.23         4.60 
TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
        0.10         0.03         9.63        58.45        25.08        19.56 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 
        7.33        10.09        10.98        20.58         2.10         6.81 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        0.16        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       43.17        21.63        40.83        30.28        26.04        13.25 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
        7.63         7.89        93.34        44.84        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 
       26.27        20.12        11.28        13.74        79.82        54.87 
TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       19.00        48.62        11.05        34.82        25.15        14.63 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-PJ-A5Z8 
        3.68         1.05         4.57        14.14         1.08         3.68 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           194.76             93.34 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           13.550            14.385 
[1] "0.0 - 194.8 (13.6)" "0.0 - 93.3 (14.4)" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
[1] "hr=" "2.4"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED        47        3        10        6
  7Q GAIN WILD-TYPE      22        7        20        4
D13V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                47                22
  STAGE II                3                 7
  STAGE III              10                20
  STAGE IV                6                 4
                   vv
clus                T1 T2 T3+T4
  7Q GAIN MUTATED   49  9    15
  7Q GAIN WILD-TYPE 25  7    24
D13V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                 49                25
  T2                  9                 7
  T3+T4              15                24
                   vv
clus                N0 N1 N2
  7Q GAIN MUTATED   12  4  2
  7Q GAIN WILD-TYPE 14  8  2
D13V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              12                14
  N1               4                 8
  N2               2                 2
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   28  3 36
  7Q GAIN WILD-TYPE 29  3 21
D13V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              28                29
  M1               3                 3
  MX              36                21
D13V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   18 55
  7Q GAIN WILD-TYPE 22 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     18   55
  7Q GAIN WILD-TYPE   22   34
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              18                22
  MALE                55                34
D13V8, continuous
D13V9, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"        "7Q GAIN WILD-TYPE"     
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                2                 2 
named character(0)
D13V10, continuous
[1] "Remove cluster labels:" "7Q GAIN MUTATED"        "7Q GAIN WILD-TYPE"     
clus
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                2                 1 
named character(0)

Clustering(14) Variable = 8P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    7  2
  8P GAIN WILD-TYPE 97 13
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9               110 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                13 
$`8P GAIN MUTATED`
TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-G7-6789 
       13.55         0.16        43.17        25.35        20.12         4.01 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 
        3.68         1.05         1.08 

$`8P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       58.45        53.79        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 
       15.12         6.44         1.18         2.10         6.81        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 
       19.23         8.84        63.72        22.92        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       19.00        24.89        51.75        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 
       34.82        25.15        14.63        14.07       194.76         7.73 
TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 
        5.85         2.99         4.57        14.14         2.04         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.16              0.03 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            43.17            194.76 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            4.010            14.105 
[1] "0.2 - 43.2 (4.0)"   "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "4.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         4        1         4        1
  8P GAIN WILD-TYPE      65        9        26        9
D14V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 4                65
  STAGE II                1                 9
  STAGE III               4                26
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  8P GAIN MUTATED    4  1     5
  8P GAIN WILD-TYPE 70 15    34
D14V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  4                70
  T2                  1                15
  T3+T4               5                34
                   vv
clus                N0 N1 N2
  8P GAIN MUTATED    2  2  1
  8P GAIN WILD-TYPE 24 10  3
D14V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0               2                24
  N1               2                10
  N2               1                 3
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED    4  0  6
  8P GAIN WILD-TYPE 53  6 51
D14V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               4                53
  M1               0                 6
  MX               6                51
D14V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  6
  8P GAIN WILD-TYPE 36 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    6
  8P GAIN WILD-TYPE   36   83
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               4                36
  MALE                 6                83
D14V8, continuous
D14V9, continuous
D14V10, continuous

Clustering(15) Variable = 8Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    8  4
  8Q GAIN WILD-TYPE 96 11
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12               107 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                11 
$`8Q GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-7056 
        9.63        13.55         0.16        43.17        25.35        20.12 
TCGA-G7-6789 TCGA-G7-6793 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y TCGA-IZ-8195 
        4.01        11.05         3.68         1.05         2.04         1.08 

$`8Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       53.79        30.31        25.08        44.61        19.56         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       16.37        10.09        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.14        26.40        20.58         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5876 
        6.44         1.18         2.10         6.81        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.84        63.72        22.92        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.74         3.75        14.63         3.02        28.80        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        34.19        19.00 
TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       24.89        51.75        48.62        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
       14.63        14.07       194.76         7.73         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.57        14.14         4.04         3.68         5.69 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.16              0.03 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            43.17            194.76 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             6.82             14.63 
[1] "0.2 - 43.2 (6.8)"   "0.0 - 194.8 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
[1] "hr=" "8.8"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         4        1         5        3
  8Q GAIN WILD-TYPE      65        9        25        7
D15V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 4                65
  STAGE II                1                 9
  STAGE III               5                25
  STAGE IV                3                 7
                   vv
clus                T1 T2 T3+T4
  8Q GAIN MUTATED    4  1     8
  8Q GAIN WILD-TYPE 70 15    31
D15V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  4                70
  T2                  1                15
  T3+T4               8                31
                   vv
clus                N0 N1 N2
  8Q GAIN MUTATED    2  4  2
  8Q GAIN WILD-TYPE 24  8  2
D15V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0               2                24
  N1               4                 8
  N2               2                 2
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED    4  1  8
  8Q GAIN WILD-TYPE 53  5 49
D15V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               4                53
  M1               1                 5
  MX               8                49
D15V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6  7
  8Q GAIN WILD-TYPE 34 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6    7
  8Q GAIN WILD-TYPE   34   82
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               6                34
  MALE                 7                82
D15V8, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                20 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-5561 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
D15V9, continuous
D15V10, continuous

Clustering(16) Variable = 10P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     3   1
  10P GAIN WILD-TYPE 101  14
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                115 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 14 
$`10P GAIN MUTATED`
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 TCGA-BQ-5882 
        4.60        53.79         1.08        21.63 

$`10P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.89         0.23         1.61         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        19.56         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       16.37        10.09        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 
       28.14        26.40        20.58         0.46        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 
        1.18         2.10         6.81         0.16        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.84        63.72        22.92        43.17        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       34.19        19.00        24.89         4.01        51.75        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        14.63        14.07 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.76         3.68         7.73         1.05         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
        4.57        14.14         2.04         1.08         4.04         3.68 
TCGA-PJ-A5Z9 
        5.69 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.08               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             53.79             194.76 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            13.115             13.740 
[1] "1.1 - 53.8 (13.1)"  "0.0 - 194.8 (13.7)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         1        1         2        0
  10P GAIN WILD-TYPE      68        9        28       10
D16V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  1                 68
  STAGE II                 1                  9
  STAGE III                2                 28
  STAGE IV                 0                 10
                    vv
clus                 T1 T2 T3+T4
  10P GAIN MUTATED    2  1     2
  10P GAIN WILD-TYPE 72 15    37
D16V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                   2                 72
  T2                   1                 15
  T3+T4                2                 37
                    vv
clus                 N0 N1 N2
  10P GAIN MUTATED    1  0  0
  10P GAIN WILD-TYPE 25 12  4
D16V5, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 41 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-AL-3466         TCGA-AL-3472 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6793 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-IA-A40U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-6720 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  10P GAIN MUTATED    4  0  1
  10P GAIN WILD-TYPE 53  6 56
D16V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                4                 53
  M1                0                  6
  MX                1                 56
D16V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  4
  10P GAIN WILD-TYPE 39 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    4
  10P GAIN WILD-TYPE   39   85
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                1                 39
  MALE                  4                 85
D16V8, continuous
D16V9, continuous
D16V10, continuous

Clustering(17) Variable = 10Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     3   0
  10Q GAIN WILD-TYPE 101  15
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                116 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                 15 
$`10Q GAIN MUTATED`
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 
        4.60        53.79         1.08 

$`10Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.89         0.23         1.61         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        19.56         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       16.37        10.09        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 
       28.14        26.40        20.58         0.46        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 
        1.18         2.10         6.81         0.16        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.84        63.72        22.92        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.37        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        28.80        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       54.87        34.19        19.00        24.89         4.01        51.75 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.07       194.76         3.68         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.08               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             53.79             194.76 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             4.600             13.905 
[1] "1.1 - 53.8 (4.6)"   "0.0 - 194.8 (13.9)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         1        1         1        0
  10Q GAIN WILD-TYPE      68        9        29       10
D17V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  1                 68
  STAGE II                 1                  9
  STAGE III                1                 29
  STAGE IV                 0                 10
                    vv
clus                 T1 T2 T3+T4
  10Q GAIN MUTATED    2  1     1
  10Q GAIN WILD-TYPE 72 15    38
D17V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                   2                 72
  T2                   1                 15
  T3+T4                1                 38
                    vv
clus                 N0 N1 N2
  10Q GAIN MUTATED    0  0  0
  10Q GAIN WILD-TYPE 26 12  4
D17V5, multiclass
                    vv
clus                 M0 M1 MX
  10Q GAIN MUTATED    3  0  1
  10Q GAIN WILD-TYPE 54  6 56
D17V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                3                 54
  M1                0                  6
  MX                1                 56
D17V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    1  3
  10Q GAIN WILD-TYPE 39 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    3
  10Q GAIN WILD-TYPE   39   86
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                1                 39
  MALE                  3                 86
D17V8, continuous
D17V9, continuous
D17V10, continuous

Clustering(18) Variable = 11P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     4   1
  11P GAIN WILD-TYPE 100  14
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                114 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 14 
$`11P GAIN MUTATED`
TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5889 TCGA-BQ-5892 TCGA-GL-7966 
        0.46         2.10        10.88        11.97         3.68 

$`11P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        53.79        13.55        30.31        25.08        44.61 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       19.56         7.33        16.37        10.09        11.41        10.98 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
        4.83        50.50        28.14        26.40        20.58         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
       15.12         6.44         1.18         6.81         0.16        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       13.25         7.63         0.95         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       34.19        19.00        24.89         4.01        51.75        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        14.63        14.07 
TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
      194.76         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         4.04         3.68         5.69 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.46               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             11.97             194.76 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             3.680             14.385 
[1] "0.5 - 12.0 (3.7)"   "0.0 - 194.8 (14.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "7"  
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         1        0         2        2
  11P GAIN WILD-TYPE      68       10        28        8
D18V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  1                 68
  STAGE II                 0                 10
  STAGE III                2                 28
  STAGE IV                 2                  8
                    vv
clus                 T1 T2 T3+T4
  11P GAIN MUTATED    1  2     3
  11P GAIN WILD-TYPE 73 14    36
D18V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                   1                 73
  T2                   2                 14
  T3+T4                3                 36
                    vv
clus                 N0 N1 N2
  11P GAIN MUTATED    2  2  0
  11P GAIN WILD-TYPE 24 10  4
D18V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0                2                 24
  N1                2                 10
  N2                0                  4
                    vv
clus                 M0 M1 MX
  11P GAIN MUTATED    1  2  1
  11P GAIN WILD-TYPE 56  4 56
D18V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                1                 56
  M1                2                  4
  MX                1                 56
D18V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  4
  11P GAIN WILD-TYPE 38 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    4
  11P GAIN WILD-TYPE   38   85
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 38
  MALE                  4                 85
D18V8, continuous
D18V9, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                  3 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-PJ-A5Z9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D18V10, continuous

Clustering(19) Variable = 11Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     3   0
  11Q GAIN WILD-TYPE 101  15
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                116 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                 15 
$`11Q GAIN MUTATED`
TCGA-B9-4117 TCGA-BQ-5892 TCGA-GL-7966 
        0.46        11.97         3.68 

$`11Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        53.79        13.55        30.31        25.08        44.61 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       19.56         7.33        16.37        10.09        11.41        10.98 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
        4.83        50.50        28.14        26.40        20.58         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12         6.44         1.18         2.10         6.81         0.16 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       25.35        13.25        10.88         7.63         0.95         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        28.80        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        34.19        19.00        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.75        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.63        14.07       194.76         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.46               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             11.97             194.76 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             3.680             14.105 
[1] "0.5 - 12.0 (3.7)"   "0.0 - 194.8 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr="     "3300000"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         1        0         1        1
  11Q GAIN WILD-TYPE      68       10        29        9
D19V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  1                 68
  STAGE II                 0                 10
  STAGE III                1                 29
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  11Q GAIN MUTATED    1  2     1
  11Q GAIN WILD-TYPE 73 14    38
D19V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                   1                 73
  T2                   2                 14
  T3+T4                1                 38
                    vv
clus                 N0 N1 N2
  11Q GAIN MUTATED    2  1  0
  11Q GAIN WILD-TYPE 24 11  4
D19V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0                2                 24
  N1                1                 11
  N2                0                  4
                    vv
clus                 M0 M1 MX
  11Q GAIN MUTATED    1  1  1
  11Q GAIN WILD-TYPE 56  5 56
D19V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                1                 56
  M1                1                  5
  MX                1                 56
D19V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  2
  11Q GAIN WILD-TYPE 38 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    2
  11Q GAIN WILD-TYPE   38   87
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                2                 38
  MALE                  2                 87
D19V8, continuous
D19V9, continuous
D19V10, continuous

Clustering(20) Variable = 12P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   39  6
  12P GAIN WILD-TYPE 65  9
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                45                 74 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                  9 
$`12P GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 
        0.03         0.03         4.60         0.03         0.72         0.03 
TCGA-A4-8518 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 TCGA-B3-3925 TCGA-B9-4113 
        0.10        53.79        13.55        44.61        16.37        50.50 
TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5877 
       28.14         1.08         6.44         1.18         0.16         8.84 
TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7059 
       43.17        25.35        10.88         0.95        11.97         7.63 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 
        7.13         3.78        13.61        37.55         3.75        14.63 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-G7-6789 TCGA-G7-6795 
       28.80        80.84        51.16        61.02         4.01        39.25 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
      194.76         3.68         1.05         5.85         2.99         4.57 
TCGA-IA-A40Y TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        2.04         3.68         5.69 

$`12P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95         0.10        35.18         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        1.61         0.07         0.69         0.03         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4103 
       30.31        25.08        19.56         7.33        10.09        11.41 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
       10.98         4.83        26.40        20.58         0.46        15.12 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
        2.10         6.81        86.73        19.23        63.72        22.92 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       13.25         7.63         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-DW-5560 TCGA-DW-7834 
       26.27        20.12        11.28         7.00        11.61       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6135 
       35.93        24.46        13.74         3.02        79.82        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       34.19        19.00        24.89        51.75        48.62        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-8500 TCGA-IA-A40X 
       34.82        25.15        14.63        14.07         7.73        14.14 
TCGA-IZ-8195 TCGA-IZ-8196 
        1.08         4.04 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.03               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            194.76             129.86 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             6.440             19.395 
[1] "0.0 - 194.8 (6.4)"  "0.0 - 129.9 (19.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" 
[1] "hr=" "1.6"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED        26        2        11        5
  12P GAIN WILD-TYPE      43        8        19        5
D20V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 26                 43
  STAGE II                 2                  8
  STAGE III               11                 19
  STAGE IV                 5                  5
                    vv
clus                 T1 T2 T3+T4
  12P GAIN MUTATED   28  4    17
  12P GAIN WILD-TYPE 46 12    22
D20V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                  28                 46
  T2                   4                 12
  T3+T4               17                 22
                    vv
clus                 N0 N1 N2
  12P GAIN MUTATED    8  6  2
  12P GAIN WILD-TYPE 18  6  2
D20V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                8                 18
  N1                6                  6
  N2                2                  2
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED   16  2 27
  12P GAIN WILD-TYPE 41  4 30
D20V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               16                 41
  M1                2                  4
  MX               27                 30
D20V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   11 38
  12P GAIN WILD-TYPE 29 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     11   38
  12P GAIN WILD-TYPE   29   51
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               11                 29
  MALE                 38                 51
D20V8, continuous
D20V9, continuous
[1] "Remove cluster labels:" "12P GAIN WILD-TYPE"    
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                  1 
      TCGA-GL-A59T       TCGA-IA-A40U       TCGA-PJ-A5Z9 
"12P GAIN MUTATED" "12P GAIN MUTATED" "12P GAIN MUTATED" 
D20V10, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"       "12P GAIN WILD-TYPE"    
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  1 
named character(0)

Clustering(21) Variable = 12Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   39  6
  12Q GAIN WILD-TYPE 65  9
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                45                 74 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                  9 
$`12Q GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 
        0.03         0.03         4.60         0.03         0.72         0.03 
TCGA-A4-8518 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 TCGA-B3-3925 TCGA-B9-4113 
        0.10        53.79        13.55        44.61        16.37        50.50 
TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5877 
       28.14         1.08         6.44         1.18         0.16         8.84 
TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7059 
       43.17        25.35        10.88         0.95        11.97         7.63 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 
        7.13         3.78        13.61        37.55         3.75        14.63 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-G7-6789 TCGA-G7-6795 
       28.80        80.84        51.16        61.02         4.01        39.25 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
      194.76         3.68         1.05         5.85         2.99         4.57 
TCGA-IA-A40Y TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        2.04         3.68         5.69 

$`12Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95         0.10        35.18         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        1.61         0.07         0.69         0.03         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4103 
       30.31        25.08        19.56         7.33        10.09        11.41 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
       10.98         4.83        26.40        20.58         0.46        15.12 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
        2.10         6.81        86.73        19.23        63.72        22.92 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       13.25         7.63         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-DW-5560 TCGA-DW-7834 
       26.27        20.12        11.28         7.00        11.61       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6135 
       35.93        24.46        13.74         3.02        79.82        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       34.19        19.00        24.89        51.75        48.62        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-8500 TCGA-IA-A40X 
       34.82        25.15        14.63        14.07         7.73        14.14 
TCGA-IZ-8195 TCGA-IZ-8196 
        1.08         4.04 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.03               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            194.76             129.86 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             6.440             19.395 
[1] "0.0 - 194.8 (6.4)"  "0.0 - 129.9 (19.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
[1] "hr=" "1.6"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED        26        2        11        5
  12Q GAIN WILD-TYPE      43        8        19        5
D21V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 26                 43
  STAGE II                 2                  8
  STAGE III               11                 19
  STAGE IV                 5                  5
                    vv
clus                 T1 T2 T3+T4
  12Q GAIN MUTATED   28  4    17
  12Q GAIN WILD-TYPE 46 12    22
D21V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                  28                 46
  T2                   4                 12
  T3+T4               17                 22
                    vv
clus                 N0 N1 N2
  12Q GAIN MUTATED    8  6  2
  12Q GAIN WILD-TYPE 18  6  2
D21V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                8                 18
  N1                6                  6
  N2                2                  2
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED   16  2 27
  12Q GAIN WILD-TYPE 41  4 30
D21V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               16                 41
  M1                2                  4
  MX               27                 30
D21V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   11 38
  12Q GAIN WILD-TYPE 29 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     11   38
  12Q GAIN WILD-TYPE   29   51
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               11                 29
  MALE                 38                 51
D21V8, continuous
D21V9, continuous
[1] "Remove cluster labels:" "12Q GAIN WILD-TYPE"    
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                  1 
      TCGA-GL-A59T       TCGA-IA-A40U       TCGA-PJ-A5Z9 
"12Q GAIN MUTATED" "12Q GAIN MUTATED" "12Q GAIN MUTATED" 
D21V10, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"       "12Q GAIN WILD-TYPE"    
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                  1 
named character(0)

Clustering(22) Variable = 13Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   12  1
  13Q GAIN WILD-TYPE 92 14
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                106 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 14 
$`13Q GAIN MUTATED`
TCGA-A4-8311 TCGA-A4-8518 TCGA-B1-5398 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 
        0.07         0.10        19.56         4.83         0.46         1.08 
TCGA-BQ-5885 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 TCGA-EV-5903 TCGA-G7-6790 
       30.28        96.92        13.61        51.16        24.89        51.75 
TCGA-G7-6796 
       34.82 

$`13Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 
        0.89         0.23         1.61         4.60         0.03         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.72         0.03         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 
       13.55        30.31        25.08        44.61         7.33        16.37 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       10.09        11.41        10.98        50.50        28.14        26.40 
TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 
       20.58        15.12         6.44         1.18         2.10         6.81 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        0.16        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
       43.17        47.80        21.63        40.83        26.04        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.63         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 
        7.89         2.76       123.58        48.26        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 
        7.63         7.00         7.13         3.78        11.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        28.80        79.82        80.84        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       34.19        19.00         4.01        48.62        11.05        39.25 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       25.15        14.63        14.07       194.76         3.68         7.73 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
        1.05         5.85         2.99         4.57        14.14         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        1.08         4.04         3.68         5.69 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.07               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             96.92             194.76 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            19.560             13.645 
[1] "0.1 - 96.9 (19.6)"  "0.0 - 194.8 (13.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED        10        0         3        0
  13Q GAIN WILD-TYPE      59       10        27       10
D22V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                 10                 59
  STAGE II                 0                 10
  STAGE III                3                 27
  STAGE IV                 0                 10
                    vv
clus                 T1 T2 T3+T4
  13Q GAIN MUTATED   11  1     3
  13Q GAIN WILD-TYPE 63 15    36
D22V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                  11                 63
  T2                   1                 15
  T3+T4                3                 36
                    vv
clus                 N0 N1 N2
  13Q GAIN MUTATED    2  0  0
  13Q GAIN WILD-TYPE 24 12  4
D22V5, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 40 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-AL-3466         TCGA-AL-3472 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B9-7268 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5882         TCGA-BQ-5887 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DW-7963         TCGA-DZ-6131 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6793         TCGA-G7-6795 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-GL-6846         TCGA-GL-7966 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-A59R         TCGA-IA-A40U         TCGA-IA-A40Y 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-J7-6720 
"13Q GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  13Q GAIN MUTATED    7  0  7
  13Q GAIN WILD-TYPE 50  6 50
D22V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                7                 50
  M1                0                  6
  MX                7                 50
D22V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5 10
  13Q GAIN WILD-TYPE 35 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   10
  13Q GAIN WILD-TYPE   35   79
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                 35
  MALE                 10                 79
D22V8, continuous
D22V9, continuous
D22V10, continuous

Clustering(23) Variable = 16P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   53  7
  16P GAIN WILD-TYPE 51  8
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                60                 59 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                  8 
$`16P GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-8310 
        0.03        15.95         0.10        35.18         1.61         0.03 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D 
        0.07         0.69         0.72         0.03         0.10         0.03 
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-5398 TCGA-B3-4103 TCGA-B3-8121 
        9.63        53.79        13.55        19.56        11.41         4.83 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       28.14         0.46         1.08        15.12         6.44         1.18 
TCGA-B9-A44B TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 
        2.10         0.16        86.73        43.17        47.80        26.04 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       25.35         7.63         0.95       123.58        48.26        96.92 
TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7836 
       50.37        11.28         7.00         3.78       129.86        35.93 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 
       24.46        28.80        51.16        61.02        19.00        24.89 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6797 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
        4.01        51.75        25.15       194.76         3.68         7.73 
TCGA-GL-A4EM TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-PJ-A5Z9 
        1.05         2.99         4.57         2.04         1.08         5.69 

$`16P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8098 TCGA-AL-3467 
        0.69         0.03         0.89         0.23         4.60        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61         7.33        16.37        10.09 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 
       10.98        50.50        26.40        20.58         6.81        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
        8.84        63.72        22.92        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        13.25        10.88        11.97         7.89         2.76 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       93.34        44.84        61.28        49.84        26.27        20.12 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 
        7.63         7.13        11.61        13.61        37.55        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
        3.75        14.63         3.02        79.82        80.84        54.87 
TCGA-EV-5901 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
       34.19        48.62        11.05        39.25        34.82        14.63 
TCGA-G7-7502 TCGA-GL-A59R TCGA-IA-A40X TCGA-IZ-8196 TCGA-PJ-A5Z8 
       14.07         5.85        14.14         4.04         3.68 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.03               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            194.76              93.34 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              8.68              14.63 
[1] "0.0 - 194.8 (8.7)" "0.0 - 93.3 (14.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED        34        4        18        4
  16P GAIN WILD-TYPE      35        6        12        6
D23V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 34                 35
  STAGE II                 4                  6
  STAGE III               18                 12
  STAGE IV                 4                  6
                    vv
clus                 T1 T2 T3+T4
  16P GAIN MUTATED   37  8    21
  16P GAIN WILD-TYPE 37  8    18
D23V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                  37                 37
  T2                   8                  8
  T3+T4               21                 18
                    vv
clus                 N0 N1 N2
  16P GAIN MUTATED   12  5  2
  16P GAIN WILD-TYPE 14  7  2
D23V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               12                 14
  N1                5                  7
  N2                2                  2
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED   25  2 33
  16P GAIN WILD-TYPE 32  4 24
D23V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               25                 32
  M1                2                  4
  MX               33                 24
D23V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   13 53
  16P GAIN WILD-TYPE 27 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     13   53
  16P GAIN WILD-TYPE   27   36
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               13                 27
  MALE                 53                 36
D23V8, continuous
D23V9, continuous
D23V10, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"       "16P GAIN WILD-TYPE"    
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                  1 
named character(0)

Clustering(24) Variable = 16Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   53  5
  16Q GAIN WILD-TYPE 51 10
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                58                 61 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 10 
$`16Q GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-8310 
        0.03        15.95         0.10        35.18         1.61         0.03 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D 
        0.07         0.69         0.72         0.03         0.10         0.03 
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-5398 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 
       53.79        13.55        19.56        11.41         4.83        28.14 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.08        15.12         6.44         1.18         2.10 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 
        0.16        86.73        43.17        47.80        26.04        25.35 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 
        0.95       123.58        48.26        96.92        50.37         7.00 
TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6133 
        3.78       129.86        35.93        24.46        28.80        51.16 
TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6797 
       61.02        19.00        24.89         4.01        51.75        25.15 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-IA-A40U 
      194.76         3.68         7.73         1.05         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         5.69 

$`16Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8098 TCGA-AL-3466 
        0.69         0.03         0.89         0.23         4.60         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 
       58.45        30.31        25.08        44.61         7.33        16.37 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 
       10.09        10.98        50.50        26.40        20.58         6.81 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 
       19.23         8.84        63.72        22.92        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       26.04        30.28        13.25        10.88         7.63        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
        7.89         2.76        93.34        44.84        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 
       26.27        20.12        11.28         7.63         7.13        11.61 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       13.61        37.55        13.74         3.75        14.63         3.02 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-G7-6792 TCGA-G7-6793 
       79.82        80.84        54.87        34.19        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-A59R TCGA-IZ-8196 
       39.25        34.82        14.63        14.07         5.85         4.04 
TCGA-PJ-A5Z8 
        3.68 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.03               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            194.76              93.34 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              9.57              14.63 
[1] "0.0 - 194.8 (9.6)" "0.0 - 93.3 (14.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
[1] "hr=" "1.7"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED        35        4        16        3
  16Q GAIN WILD-TYPE      34        6        14        7
D24V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 35                 34
  STAGE II                 4                  6
  STAGE III               16                 14
  STAGE IV                 3                  7
                    vv
clus                 T1 T2 T3+T4
  16Q GAIN MUTATED   38  8    18
  16Q GAIN WILD-TYPE 36  8    21
D24V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                  38                 36
  T2                   8                  8
  T3+T4               18                 21
                    vv
clus                 N0 N1 N2
  16Q GAIN MUTATED   11  4  1
  16Q GAIN WILD-TYPE 15  8  3
D24V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               11                 15
  N1                4                  8
  N2                1                  3
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED   23  1 34
  16Q GAIN WILD-TYPE 34  5 23
D24V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               23                 34
  M1                1                  5
  MX               34                 23
D24V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   14 50
  16Q GAIN WILD-TYPE 26 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     14   50
  16Q GAIN WILD-TYPE   26   39
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               14                 26
  MALE                 50                 39
D24V8, continuous
D24V9, continuous
D24V10, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"       "16Q GAIN WILD-TYPE"    
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                  1 
named character(0)

Clustering(25) Variable = 17P GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   61  4
  17P GAIN WILD-TYPE 43 11
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                65                 54 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 11 
$`17P GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 
        0.03        15.95         0.03         0.89         1.61         0.03 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-AL-3468 
        0.07         0.69         0.72         0.03         0.10        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
       13.55        30.31         7.33        16.37        11.41         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.14        26.40         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 
        6.44         1.18         0.16        47.80        25.35         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 
       11.97         7.89        48.26        96.92        50.37         7.00 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6795 
       51.16        61.02        34.19        24.89        51.75        39.25 
TCGA-G7-6796 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       34.82       194.76         3.68         1.05         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z9 
        4.57         2.04         1.08         4.04         5.69 

$`17P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A48D 
        0.69         0.10        35.18         0.23         4.60         0.03 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 
        9.63        58.45        25.08        44.61        19.56        10.09 
TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5876 
       10.98        20.58         2.10         6.81        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.84        63.72        22.92        43.17        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.88         7.63 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
        2.76       123.58        93.34        44.84        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 
       26.27        20.12        11.28         7.63         7.13        79.82 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       80.84        54.87        19.00         4.01        48.62        11.05 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-8500 TCGA-IA-A40X TCGA-PJ-A5Z8 
       25.15        14.63        14.07         7.73        14.14         3.68 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.03               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            194.76             123.58 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            11.410             19.395 
[1] "0.0 - 194.8 (11.4)" "0.0 - 123.6 (19.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
[1] "hr=" "2.4"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED        46        5        10        2
  17P GAIN WILD-TYPE      23        5        20        8
D25V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                 46                 23
  STAGE II                 5                  5
  STAGE III               10                 20
  STAGE IV                 2                  8
                    vv
clus                 T1 T2 T3+T4
  17P GAIN MUTATED   48 10    13
  17P GAIN WILD-TYPE 26  6    26
D25V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                  48                 26
  T2                  10                  6
  T3+T4               13                 26
                    vv
clus                 N0 N1 N2
  17P GAIN MUTATED   12  4  0
  17P GAIN WILD-TYPE 14  8  4
D25V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               12                 14
  N1                4                  8
  N2                0                  4
                    vv
clus                 M0 M1 MX
  17P GAIN MUTATED   22  1 41
  17P GAIN WILD-TYPE 35  5 16
D25V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               22                 35
  M1                1                  5
  MX               41                 16
D25V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   16 55
  17P GAIN WILD-TYPE 24 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     16   55
  17P GAIN WILD-TYPE   24   34
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               16                 24
  MALE                 55                 34
D25V8, continuous
D25V9, continuous
[1] "Remove cluster labels:" "17P GAIN WILD-TYPE"    
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                  1 
      TCGA-GL-A59T       TCGA-IA-A40U       TCGA-PJ-A5Z9 
"17P GAIN MUTATED" "17P GAIN MUTATED" "17P GAIN MUTATED" 
D25V10, continuous

Clustering(26) Variable = 17Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   69  8
  17Q GAIN WILD-TYPE 35  7
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                77                 42 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                  7 
$`17Q GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.03        15.95         0.03         0.89         0.23         1.61 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
        0.03         0.07         0.69         0.72         0.03         0.10 
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B1-7332 TCGA-B3-3925 
        9.63        53.79        13.55        30.31         7.33        16.37 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       11.41         4.83        50.50        28.14        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W9 
        1.08        15.12         6.44         1.18         2.10         0.16 
TCGA-BQ-5875 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
       86.73        47.80        26.04        25.35        13.25         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 
        0.95        11.97         7.89        48.26        96.92        50.37 
TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       49.84        11.28         7.00         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        28.80        80.84        51.16        61.02 
TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 
       34.19        24.89         4.01        51.75        11.05        39.25 
TCGA-G7-6796 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       34.82       194.76         3.68         1.05         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z9 
        4.57         2.04         1.08         4.04         5.69 

$`17Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.10        35.18         4.60         0.03        58.45 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 
       25.08        44.61        19.56        10.09        10.98        20.58 
TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        6.81        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 
       21.63        40.83        26.04        30.28        10.88         2.76 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7056 
      123.58        93.34        44.84        61.28        26.27        20.12 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6792 
        7.63         7.13        79.82        54.87        19.00        48.62 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-8500 TCGA-IA-A40X TCGA-PJ-A5Z8 
       25.15        14.63        14.07         7.73        14.14         3.68 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.03               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            194.76             123.58 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             11.28              20.35 
[1] "0.0 - 194.8 (11.3)" "0.0 - 123.6 (20.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED        48        6        16        6
  17Q GAIN WILD-TYPE      21        4        14        4
D26V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                 48                 21
  STAGE II                 6                  4
  STAGE III               16                 14
  STAGE IV                 6                  4
                    vv
clus                 T1 T2 T3+T4
  17Q GAIN MUTATED   50 12    22
  17Q GAIN WILD-TYPE 24  4    17
D26V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                  50                 24
  T2                  12                  4
  T3+T4               22                 17
                    vv
clus                 N0 N1 N2
  17Q GAIN MUTATED   16  5  3
  17Q GAIN WILD-TYPE 10  7  1
D26V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               16                 10
  N1                5                  7
  N2                3                  1
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   28  3 45
  17Q GAIN WILD-TYPE 29  3 12
D26V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               28                 29
  M1                3                  3
  MX               45                 12
D26V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   22 62
  17Q GAIN WILD-TYPE 18 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     22   62
  17Q GAIN WILD-TYPE   18   27
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               22                 18
  MALE                 62                 27
D26V8, continuous
D26V9, continuous
D26V10, continuous

Clustering(27) Variable = 18P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    5  1
  18P GAIN WILD-TYPE 99 14
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                113 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 14 
$`18P GAIN MUTATED`
TCGA-AL-3466 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 TCGA-DW-5560 TCGA-G7-6790 
        9.63        11.41        10.98        15.12        11.61        51.75 

$`18P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        7.33        16.37        10.09         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.58         0.46         1.08         6.44         1.18 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        2.10         6.81         0.16        86.73        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.17        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.13         3.78        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       19.00        24.89         4.01        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       34.82        25.15        14.63        14.07       194.76         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X 
        7.73         1.05         5.85         2.99         4.57        14.14 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        2.04         1.08         4.04         3.68         5.69 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              9.63               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             51.75             194.76 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             11.51              14.07 
[1] "9.6 - 51.8 (11.5)"  "0.0 - 194.8 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         3        1         2        1
  18P GAIN WILD-TYPE      66        9        28        9
D27V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  3                 66
  STAGE II                 1                  9
  STAGE III                2                 28
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  18P GAIN MUTATED    3  1     3
  18P GAIN WILD-TYPE 71 15    36
D27V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   3                 71
  T2                   1                 15
  T3+T4                3                 36
                    vv
clus                 N0 N1 N2
  18P GAIN MUTATED    0  1  0
  18P GAIN WILD-TYPE 26 11  4
D27V5, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 41 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-AL-3472         TCGA-AL-3473 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B9-7268 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5882         TCGA-BQ-5885 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6793 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-IA-A40U 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-6720 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  18P GAIN MUTATED    4  1  1
  18P GAIN WILD-TYPE 53  5 56
D27V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                4                 53
  M1                1                  5
  MX                1                 56
D27V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    2  5
  18P GAIN WILD-TYPE 38 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    5
  18P GAIN WILD-TYPE   38   84
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                2                 38
  MALE                  5                 84
D27V8, continuous
D27V9, continuous
D27V10, continuous

Clustering(28) Variable = 18Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    5  0
  18Q GAIN WILD-TYPE 99 15
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                114 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 15 
$`18Q GAIN MUTATED`
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 TCGA-DW-5560 TCGA-G7-6790 
       11.41        10.98        15.12        11.61        51.75 

$`18Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        53.79        13.55        30.31        25.08        44.61 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 TCGA-B9-4113 
       19.56         7.33        16.37        10.09         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.14        26.40        20.58         0.46         1.08         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 
        1.18         2.10         6.81         0.16        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.84        63.72        22.92        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.37        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.00         7.13         3.78        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       34.19        19.00        24.89         4.01        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       39.25        34.82        25.15        14.63        14.07       194.76 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
        3.68         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         4.04         3.68         5.69 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             10.98               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             51.75             194.76 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            11.610             13.905 
[1] "11.0 - 51.8 (11.6)" "0.0 - 194.8 (13.9)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr="     "2.7e+07"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         3        1         1        0
  18Q GAIN WILD-TYPE      66        9        29       10
D28V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  3                 66
  STAGE II                 1                  9
  STAGE III                1                 29
  STAGE IV                 0                 10
                    vv
clus                 T1 T2 T3+T4
  18Q GAIN MUTATED    3  1     1
  18Q GAIN WILD-TYPE 71 15    38
D28V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   3                 71
  T2                   1                 15
  T3+T4                1                 38
                    vv
clus                 N0 N1 N2
  18Q GAIN MUTATED    0  0  0
  18Q GAIN WILD-TYPE 26 12  4
D28V5, multiclass
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED    3  0  1
  18Q GAIN WILD-TYPE 54  6 56
D28V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                3                 54
  M1                0                  6
  MX                1                 56
D28V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  4
  18Q GAIN WILD-TYPE 39 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    4
  18Q GAIN WILD-TYPE   39   85
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 39
  MALE                  4                 85
D28V8, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 20 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D28V9, continuous
D28V10, continuous

Clustering(29) Variable = 20P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   37  4
  20P GAIN WILD-TYPE 67 11
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                41                 78 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 4                 11 
$`20P GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
        0.03         0.03         0.89         1.61         0.03         0.07 
TCGA-A4-8517 TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-7332 
        0.03         0.10         9.63        53.79        13.55         7.33 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 
       16.37        11.41         4.83         0.46         1.08         1.18 
TCGA-B9-A5W9 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
        0.16        21.63        25.35         0.95        11.97         2.76 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 
       96.92        50.37         3.78        11.61        13.61        35.93 
TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6795 
       14.63        80.84        51.16        19.00         4.01        39.25 
TCGA-G7-6797 TCGA-GL-7966 TCGA-IA-A40Y TCGA-IZ-8195 TCGA-PJ-A5Z9 
       25.15         3.68         2.04         1.08         5.69 

$`20P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
        0.69        15.95         0.10        35.18         0.23         4.60 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        0.69         0.72         0.03        58.45        30.31        25.08 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       44.61        19.56        10.09        10.98        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W8 
       26.40        20.58        15.12         6.44         2.10         6.81 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       47.80        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       10.88         7.63         7.89       123.58        48.26        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        7.63         7.00         7.13       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 
       13.74         3.75         3.02        28.80        79.82        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       54.87        34.19        24.89        51.75        48.62        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM 
       34.82        14.63        14.07       194.76         7.73         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 TCGA-PJ-A5Z8 
        5.85         2.99         4.57        14.14         4.04         3.68 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.03               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             96.92             194.76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              5.69              19.84 
[1] "0.0 - 96.9 (5.7)"   "0.0 - 194.8 (19.8)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        22        5         8        3
  20P GAIN WILD-TYPE      47        5        22        7
D29V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 22                 47
  STAGE II                 5                  5
  STAGE III                8                 22
  STAGE IV                 3                  7
                    vv
clus                 T1 T2 T3+T4
  20P GAIN MUTATED   24  7    11
  20P GAIN WILD-TYPE 50  9    28
D29V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                  24                 50
  T2                   7                  9
  T3+T4               11                 28
                    vv
clus                 N0 N1 N2
  20P GAIN MUTATED    7  4  1
  20P GAIN WILD-TYPE 19  8  3
D29V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                7                 19
  N1                4                  8
  N2                1                  3
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED   16  2 22
  20P GAIN WILD-TYPE 41  4 35
D29V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               16                 41
  M1                2                  4
  MX               22                 35
D29V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   12 30
  20P GAIN WILD-TYPE 28 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12   30
  20P GAIN WILD-TYPE   28   59
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               12                 28
  MALE                 30                 59
D29V8, continuous
D29V9, continuous
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  3 
        TCGA-B9-A44B         TCGA-GL-A59T         TCGA-IA-A40U 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
D29V10, continuous
[1] "Remove cluster labels:" "20P GAIN MUTATED"       "20P GAIN WILD-TYPE"    
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  2 
named character(0)

Clustering(30) Variable = 20Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   38  5
  20Q GAIN WILD-TYPE 66 10
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                 76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                 10 
$`20Q GAIN MUTATED`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
        0.03         0.03         0.89         1.61         0.03         0.07 
TCGA-A4-8517 TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-7332 
        0.03         0.10         9.63        53.79        13.55         7.33 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 
       16.37        11.41        10.98         4.83         0.46         1.08 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5891 
        1.18         0.16        22.92        21.63        25.35         0.95 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 
       11.97         2.76        96.92        50.37         3.78        11.61 
TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 
       13.61        35.93        14.63        80.84        51.16        19.00 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-7966 TCGA-IA-A40Y TCGA-IZ-8195 
        4.01        39.25        25.15         3.68         2.04         1.08 
TCGA-PJ-A5Z9 
        5.69 

$`20Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
        0.69        15.95         0.10        35.18         0.23         4.60 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        0.69         0.72         0.03        58.45        30.31        25.08 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       44.61        19.56        10.09        50.50        28.14        26.40 
TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 
       20.58        15.12         6.44         2.10         6.81        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.23         8.84        63.72        43.17        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.88         7.63 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        7.89       123.58        48.26        93.34        44.84        61.28 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        7.13       129.86        37.55        24.46        13.74         3.75 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        28.80        79.82        61.02        54.87        34.19 
TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 
       24.89        51.75        48.62        11.05        34.82        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       14.07       194.76         7.73         1.05         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8196 TCGA-PJ-A5Z8 
        4.57        14.14         4.04         3.68 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.03               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             96.92             194.76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              7.33              19.84 
[1] "0.0 - 96.9 (7.3)"   "0.0 - 194.8 (19.8)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
[1] "hr=" "1.5"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        22        6        10        3
  20Q GAIN WILD-TYPE      47        4        20        7
D30V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 22                 47
  STAGE II                 6                  4
  STAGE III               10                 20
  STAGE IV                 3                  7
                    vv
clus                 T1 T2 T3+T4
  20Q GAIN MUTATED   24  8    13
  20Q GAIN WILD-TYPE 50  8    26
D30V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                  24                 50
  T2                   8                  8
  T3+T4               13                 26
                    vv
clus                 N0 N1 N2
  20Q GAIN MUTATED    7  5  1
  20Q GAIN WILD-TYPE 19  7  3
D30V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                7                 19
  N1                5                  7
  N2                1                  3
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   19  2 22
  20Q GAIN WILD-TYPE 38  4 35
D30V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               19                 38
  M1                2                  4
  MX               22                 35
D30V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   14 31
  20Q GAIN WILD-TYPE 26 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     14   31
  20Q GAIN WILD-TYPE   26   58
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               14                 26
  MALE                 31                 58
D30V8, continuous
D30V9, continuous
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  3 
        TCGA-B9-A44B         TCGA-GL-A59T         TCGA-IA-A40U 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
D30V10, continuous
[1] "Remove cluster labels:" "20Q GAIN MUTATED"       "20Q GAIN WILD-TYPE"    
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  2 
named character(0)

Clustering(31) Variable = 21Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    5  0
  21Q GAIN WILD-TYPE 99 15
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                114 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                 15 
$`21Q GAIN MUTATED`
TCGA-A4-8311 TCGA-A4-8515 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5892 
        0.07         0.69         0.46         0.16        11.97 

$`21Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 
        0.89         0.23         1.61         4.60         0.03         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        19.56         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       16.37        10.09        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.14        26.40        20.58         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        1.18         2.10         6.81        86.73        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.17        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.63         0.95         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00        24.89         4.01        51.75        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       39.25        34.82        25.15        14.63        14.07       194.76 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
        3.68         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         4.04         3.68         5.69 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             11.97             194.76 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             0.460             14.385 
[1] "0.1 - 12.0 (0.5)"   "0.0 - 194.8 (14.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr="     "3300000"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         5        0         0        0
  21Q GAIN WILD-TYPE      64       10        30       10
D31V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  5                 64
  STAGE II                 0                 10
  STAGE III                0                 30
  STAGE IV                 0                 10
                    vv
clus                 T1 T2 T3+T4
  21Q GAIN MUTATED    5  1     0
  21Q GAIN WILD-TYPE 69 15    39
D31V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                   5                 69
  T2                   1                 15
  T3+T4                0                 39
                    vv
clus                 N0 N1 N2
  21Q GAIN MUTATED    1  0  0
  21Q GAIN WILD-TYPE 25 12  4
D31V5, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 41 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-A4-A57E         TCGA-AL-3466         TCGA-AL-3472 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6793 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-GL-6846 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-IA-A40U 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-6720 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  21Q GAIN MUTATED    1  0  4
  21Q GAIN WILD-TYPE 56  6 53
D31V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                1                 56
  M1                0                  6
  MX                4                 53
D31V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    1  5
  21Q GAIN WILD-TYPE 39 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1    5
  21Q GAIN WILD-TYPE   39   84
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                1                 39
  MALE                  5                 84
D31V8, continuous
D31V9, continuous
D31V10, continuous

Clustering(32) Variable = XQ GAIN MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   29  5
  XQ GAIN WILD-TYPE 75 10
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34                85 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5                10 
$`XQ GAIN MUTATED`
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A48D TCGA-AL-3468 
        0.07         0.69         0.72         0.03         0.03        53.79 
TCGA-AL-3471 TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-4117 
       13.55        11.41        50.50        28.14        20.58         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-BQ-5881 TCGA-BQ-5887 
        1.08         6.44         1.18         2.10        47.80        25.35 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 
        0.95         7.89        48.26        96.92         7.00         3.78 
TCGA-DW-7836 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6133 TCGA-G7-6789 TCGA-G7-6790 
       35.93        14.63        28.80        51.16         4.01        51.75 
TCGA-G7-6795 TCGA-GL-6846 TCGA-GL-A59T TCGA-PJ-A5Z9 
       39.25       194.76         2.99         5.69 

$`XQ GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8518 
        0.89         0.23         1.61         4.60         0.03         0.10 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
        9.63        58.45        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
        7.33        16.37        10.09        10.98         4.83        26.40 
TCGA-B9-5155 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       15.12         6.81         0.16        86.73        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.17        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       30.28        26.04        13.25        10.88         7.63        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.58        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 
       49.84        26.27        20.12        11.28         7.63         7.13 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
        3.75         3.02        79.82        80.84        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       34.19        19.00        24.89        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       25.15        14.63        14.07         3.68         7.73         1.05 
TCGA-GL-A59R TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.85         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 
        3.68 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.03              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           194.76            129.86 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             9.65             14.14 
[1] "0.0 - 194.8 (9.7)"  "0.0 - 129.9 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
[1] "hr=" "1.3"
D32V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        24        2         4        3
  XQ GAIN WILD-TYPE      45        8        26        7
D32V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                24                45
  STAGE II                2                 8
  STAGE III               4                26
  STAGE IV                3                 7
                   vv
clus                T1 T2 T3+T4
  XQ GAIN MUTATED   25  6     7
  XQ GAIN WILD-TYPE 49 10    32
D32V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1                 25                49
  T2                  6                10
  T3+T4               7                32
                   vv
clus                N0 N1 N2
  XQ GAIN MUTATED    6  2  1
  XQ GAIN WILD-TYPE 20 10  3
D32V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0               6                20
  N1               2                10
  N2               1                 3
                   vv
clus                M0 M1 MX
  XQ GAIN MUTATED   13  1 18
  XQ GAIN WILD-TYPE 44  5 39
D32V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              13                44
  M1               1                 5
  MX              18                39
D32V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    8 30
  XQ GAIN WILD-TYPE 32 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      8   30
  XQ GAIN WILD-TYPE   32   59
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               8                32
  MALE                30                59
D32V8, continuous
D32V9, continuous
[1] "Remove cluster labels:" "XQ GAIN WILD-TYPE"     
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3                 1 
     TCGA-B9-A44B      TCGA-GL-A59T      TCGA-PJ-A5Z9 
"XQ GAIN MUTATED" "XQ GAIN MUTATED" "XQ GAIN MUTATED" 
D32V10, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"        "XQ GAIN WILD-TYPE"     
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 2 
named character(0)

Clustering(33) Variable = 1P LOSS MUTATION ANALYSIS
D33V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   16  1
  1P LOSS WILD-TYPE 88 14
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               17               102 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                14 
$`1P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-A5W8 
        0.03         0.10         4.60         7.33        10.09         6.81 
TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7055 TCGA-G7-6797 
       86.73        21.63         2.76       123.58        26.27        25.15 
TCGA-G7-7502 TCGA-GL-7966 TCGA-GL-8500 TCGA-IA-A40Y TCGA-PJ-A5Z8 
       14.07         3.68         7.73         2.04         3.68 

$`1P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
        1.61         0.03         0.07         0.69         0.72         0.03 
TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        0.10         0.03         9.63        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 
       30.31        25.08        44.61        19.56        16.37        11.41 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       10.98         4.83        50.50        28.14        26.40        20.58 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.08        15.12         6.44         1.18         2.10 
TCGA-B9-A5W9 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        0.16        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.63         0.95        11.97         7.89 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00        24.89         4.01        51.75        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-A4EM TCGA-GL-A59R 
       39.25        34.82        14.63       194.76         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z9 
        2.99         4.57        14.14         1.08         4.04         5.69 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.03              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           123.58            194.76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             7.33             14.63 
[1] "0.0 - 123.6 (7.3)"  "0.0 - 194.8 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D33V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         7        2         6        1
  1P LOSS WILD-TYPE      62        8        24        9
D33V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 7                62
  STAGE II                2                 8
  STAGE III               6                24
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  1P LOSS MUTATED    8  2     7
  1P LOSS WILD-TYPE 66 14    32
D33V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                  8                66
  T2                  2                14
  T3+T4               7                32
                   vv
clus                N0 N1 N2
  1P LOSS MUTATED    2  3  0
  1P LOSS WILD-TYPE 24  9  4
D33V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               2                24
  N1               3                 9
  N2               0                 4
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED    8  1  7
  1P LOSS WILD-TYPE 49  5 50
D33V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               8                49
  M1               1                 5
  MX               7                50
D33V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    6 11
  1P LOSS WILD-TYPE 34 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6   11
  1P LOSS WILD-TYPE   34   78
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               6                34
  MALE                11                78
D33V8, continuous
D33V9, continuous
D33V10, continuous

Clustering(34) Variable = 1Q LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   10  0
  1Q LOSS WILD-TYPE 94 15
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               109 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                15 
$`1Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5894 
        0.03         0.10         7.33        10.09         6.81         2.76 
TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-8500 TCGA-PJ-A5Z8 
       25.15        14.07         7.73         3.68 

$`1Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        19.56        16.37 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       11.41        10.98         4.83        50.50        28.14        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.58         0.46         1.08        15.12         6.44         1.18 
TCGA-B9-A44B TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        2.10         0.16        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.89       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.74         3.75        14.63         3.02        28.80        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        34.19        19.00 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       24.89         4.01        51.75        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R 
       34.82        14.63       194.76         3.68         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z9 
        5.69 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.03              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            25.15            194.76 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             7.07             14.63 
[1] "0.0 - 25.1 (7.1)"   "0.0 - 194.8 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
[1] "hr="     "2.6e+07"
D34V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         5        2         1        1
  1Q LOSS WILD-TYPE      64        8        29        9
D34V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 5                64
  STAGE II                2                 8
  STAGE III               1                29
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  1Q LOSS MUTATED    6  2     2
  1Q LOSS WILD-TYPE 68 14    37
D34V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1                  6                68
  T2                  2                14
  T3+T4               2                37
                   vv
clus                N0 N1 N2
  1Q LOSS MUTATED    1  1  0
  1Q LOSS WILD-TYPE 25 11  4
D34V5, multiclass
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                40 
       TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E        TCGA-AL-3466 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-7045        TCGA-BQ-7048 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846        TCGA-GL-7966 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                M0 M1 MX
  1Q LOSS MUTATED    4  1  4
  1Q LOSS WILD-TYPE 53  5 53
D34V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               4                53
  M1               1                 5
  MX               4                53
D34V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    3  7
  1Q LOSS WILD-TYPE 37 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    7
  1Q LOSS WILD-TYPE   37   82
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3                37
  MALE                 7                82
D34V8, continuous
D34V9, continuous
D34V10, continuous

Clustering(35) Variable = 3P LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    6  2
  3P LOSS WILD-TYPE 98 13
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8               111 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                13 
$`3P LOSS MUTATED`
TCGA-AL-3473 TCGA-B9-A44B TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5892 TCGA-DZ-6131 
       25.08         2.10         8.84        21.63        11.97        79.82 
TCGA-GL-7966 TCGA-IA-A40Y 
        3.68         2.04 

$`3P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
       15.12         6.44         1.18         6.81         0.16        86.73 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.23        63.72        22.92        43.17        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.63         0.95         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        34.19        19.00 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       24.89         4.01        51.75        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 
       34.82        25.15        14.63        14.07       194.76         7.73 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
        1.05         5.85         2.99         4.57        14.14         1.08 
TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.04         3.68         5.69 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2.04              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            79.82            194.76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           10.405            14.070 
[1] "2.0 - 79.8 (10.4)"  "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "2.7"
D35V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         1        1         5        2
  3P LOSS WILD-TYPE      68        9        25        8
D35V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1                68
  STAGE II                1                 9
  STAGE III               5                25
  STAGE IV                2                 8
                   vv
clus                T1 T2 T3+T4
  3P LOSS MUTATED    1  2     6
  3P LOSS WILD-TYPE 73 14    33
D35V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  1                73
  T2                  2                14
  T3+T4               6                33
                   vv
clus                N0 N1 N2
  3P LOSS MUTATED    5  3  0
  3P LOSS WILD-TYPE 21  9  4
D35V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               5                21
  N1               3                 9
  N2               0                 4
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED    3  2  3
  3P LOSS WILD-TYPE 54  4 54
D35V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               3                54
  M1               2                 4
  MX               3                54
D35V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    2  7
  3P LOSS WILD-TYPE 38 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    7
  3P LOSS WILD-TYPE   38   82
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               2                38
  MALE                 7                82
D35V8, continuous
D35V9, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 3 
       TCGA-GL-A59T        TCGA-IA-A40U        TCGA-PJ-A5Z9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D35V10, continuous

Clustering(36) Variable = 3Q LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     1   2
  3Q LOSS WILD-TYPE 103  13
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               116 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                13 
$`3Q LOSS MUTATED`
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-GL-7966 
        8.84        21.63         3.68 

$`3Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        53.79        13.55        30.31        25.08        44.61 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       19.56         7.33        16.37        10.09        11.41        10.98 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
        4.83        50.50        28.14        26.40        20.58         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 
        1.08        15.12         6.44         1.18         2.10         6.81 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        0.16        86.73        19.23        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        28.80        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        34.19        19.00        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.75        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.63        14.07       194.76         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3.68              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            21.63            194.76 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            8.840            13.905 
[1] "3.7 - 21.6 (8.8)"   "0.0 - 194.8 (13.9)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "17" 
D36V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         0        0         2        1
  3Q LOSS WILD-TYPE      69       10        28        9
D36V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 0                69
  STAGE II                0                10
  STAGE III               2                28
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  3Q LOSS MUTATED    0  0     3
  3Q LOSS WILD-TYPE 74 16    36
D36V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1                  0                74
  T2                  0                16
  T3+T4               3                36
                   vv
clus                N0 N1 N2
  3Q LOSS MUTATED    1  2  0
  3Q LOSS WILD-TYPE 25 10  4
D36V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               1                25
  N1               2                10
  N2               0                 4
                   vv
clus                M0 M1 MX
  3Q LOSS MUTATED    1  1  1
  3Q LOSS WILD-TYPE 56  5 56
D36V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               1                56
  M1               1                 5
  MX               1                56
D36V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    1  2
  3Q LOSS WILD-TYPE 39 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    2
  3Q LOSS WILD-TYPE   39   87
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               1                39
  MALE                 2                87
D36V8, continuous
D36V9, continuous
D36V10, continuous

Clustering(37) Variable = 4P LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    8  2
  4P LOSS WILD-TYPE 96 13
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10               109 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                13 
$`4P LOSS MUTATED`
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5894 
        0.69         7.33        10.09        22.92        21.63         2.76 
TCGA-DZ-6131 TCGA-G7-7501 TCGA-GL-7966 TCGA-IA-A40Y 
       79.82        14.63         3.68         2.04 

$`4P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       16.37        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.58         0.46         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 
        1.18         2.10         6.81         0.16        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        8.84        63.72        43.17        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.89       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        28.80        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        34.19        19.00        24.89 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.75        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       25.15        14.07       194.76         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
        2.99         4.57        14.14         1.08         4.04         3.68 
TCGA-PJ-A5Z9 
        5.69 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.69              0.03 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            79.82            194.76 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             8.71             14.07 
[1] "0.7 - 79.8 (8.7)"   "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D37V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         2        1         7        1
  4P LOSS WILD-TYPE      67        9        23        9
D37V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 2                67
  STAGE II                1                 9
  STAGE III               7                23
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  4P LOSS MUTATED    2  1     8
  4P LOSS WILD-TYPE 72 15    31
D37V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                  2                72
  T2                  1                15
  T3+T4               8                31
                   vv
clus                N0 N1 N2
  4P LOSS MUTATED    2  5  0
  4P LOSS WILD-TYPE 24  7  4
D37V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0               2                24
  N1               5                 7
  N2               0                 4
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED    4  1  6
  4P LOSS WILD-TYPE 53  5 51
D37V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               4                53
  M1               1                 5
  MX               6                51
D37V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    8  3
  4P LOSS WILD-TYPE 32 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    3
  4P LOSS WILD-TYPE   32   86
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               8                32
  MALE                 3                86
D37V8, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-7502 
"4P LOSS WILD-TYPE" 
D37V9, continuous
D37V10, continuous

Clustering(38) Variable = 4Q LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    9  1
  4Q LOSS WILD-TYPE 95 14
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               109 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                14 
$`4Q LOSS MUTATED`
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-BQ-5894 
        0.69         7.33        10.09        19.23        21.63         2.76 
TCGA-DZ-6131 TCGA-G7-7501 TCGA-GL-7966 TCGA-IA-A40Y 
       79.82        14.63         3.68         2.04 

$`4Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       16.37        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.58         0.46         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5877 
        1.18         2.10         6.81         0.16        86.73         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.17        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.89       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        28.80        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        34.19        19.00        24.89 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.75        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       25.15        14.07       194.76         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
        2.99         4.57        14.14         1.08         4.04         3.68 
TCGA-PJ-A5Z9 
        5.69 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.69              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            79.82            194.76 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             8.71             14.07 
[1] "0.7 - 79.8 (8.7)"   "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         3        1         6        2
  4Q LOSS WILD-TYPE      66        9        24        8
D38V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 3                66
  STAGE II                1                 9
  STAGE III               6                24
  STAGE IV                2                 8
                   vv
clus                T1 T2 T3+T4
  4Q LOSS MUTATED    3  2     7
  4Q LOSS WILD-TYPE 71 14    32
D38V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                  3                71
  T2                  2                14
  T3+T4               7                32
                   vv
clus                N0 N1 N2
  4Q LOSS MUTATED    3  4  0
  4Q LOSS WILD-TYPE 23  8  4
D38V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0               3                23
  N1               4                 8
  N2               0                 4
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED    4  2  6
  4Q LOSS WILD-TYPE 53  4 51
D38V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               4                53
  M1               2                 4
  MX               6                51
D38V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    7  5
  4Q LOSS WILD-TYPE 33 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      7    5
  4Q LOSS WILD-TYPE   33   84
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               7                33
  MALE                 5                84
D38V8, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-7502 
"4Q LOSS WILD-TYPE" 
D38V9, continuous
D38V10, continuous

Clustering(39) Variable = 5P LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     4   2
  5P LOSS WILD-TYPE 100  13
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6               113 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                13 
$`5P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-BQ-5879 TCGA-BQ-5894 TCGA-G7-6793 TCGA-GL-7966 
        0.03         0.69        22.92         2.76        11.05         3.68 

$`5P LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        19.56         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       16.37        10.09        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.14        26.40        20.58         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
        6.44         1.18         2.10         6.81         0.16        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.23         8.84        63.72        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 
       10.88         7.63         0.95        11.97         7.89       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       34.19        19.00        24.89         4.01        51.75        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       39.25        34.82        25.15        14.63        14.07       194.76 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X 
        7.73         1.05         5.85         2.99         4.57        14.14 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        2.04         1.08         4.04         3.68         5.69 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.03              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            22.92            194.76 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.22             14.14 
[1] "0.0 - 22.9 (3.2)"   "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "11" 
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         1        0         2        2
  5P LOSS WILD-TYPE      68       10        28        8
D39V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 1                68
  STAGE II                0                10
  STAGE III               2                28
  STAGE IV                2                 8
                   vv
clus                T1 T2 T3+T4
  5P LOSS MUTATED    1  0     5
  5P LOSS WILD-TYPE 73 16    34
D39V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  1                73
  T2                  0                16
  T3+T4               5                34
                   vv
clus                N0 N1 N2
  5P LOSS MUTATED    0  3  1
  5P LOSS WILD-TYPE 26  9  3
D39V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0               0                26
  N1               3                 9
  N2               1                 3
                   vv
clus                M0 M1 MX
  5P LOSS MUTATED    1  1  3
  5P LOSS WILD-TYPE 56  5 54
D39V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               1                56
  M1               1                 5
  MX               3                54
D39V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    4  2
  5P LOSS WILD-TYPE 36 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    2
  5P LOSS WILD-TYPE   36   87
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               4                36
  MALE                 2                87
D39V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                20 
       TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
D39V9, continuous
D39V10, continuous

Clustering(40) Variable = 5Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     4   1
  5Q LOSS WILD-TYPE 100  14
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5               114 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                14 
$`5Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-BQ-5879 TCGA-BQ-5894 TCGA-GL-7966 
        0.03         0.69        22.92         2.76         3.68 

$`5Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        19.56         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       16.37        10.09        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.14        26.40        20.58         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
        6.44         1.18         2.10         6.81         0.16        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.23         8.84        63.72        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 
       10.88         7.63         0.95        11.97         7.89       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       34.19        19.00        24.89         4.01        51.75        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        14.63        14.07 
TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
      194.76         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         4.04         3.68         5.69 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.03              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            22.92            194.76 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            2.760            14.105 
[1] "0.0 - 22.9 (2.8)"   "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "8"  
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         1        0         2        1
  5Q LOSS WILD-TYPE      68       10        28        9
D40V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 1                68
  STAGE II                0                10
  STAGE III               2                28
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  5Q LOSS MUTATED    1  0     4
  5Q LOSS WILD-TYPE 73 16    35
D40V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  1                73
  T2                  0                16
  T3+T4               4                35
                   vv
clus                N0 N1 N2
  5Q LOSS MUTATED    0  3  0
  5Q LOSS WILD-TYPE 26  9  4
D40V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               0                26
  N1               3                 9
  N2               0                 4
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED    1  1  2
  5Q LOSS WILD-TYPE 56  5 55
D40V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               1                56
  M1               1                 5
  MX               2                55
D40V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    3  2
  5Q LOSS WILD-TYPE 37 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    2
  5Q LOSS WILD-TYPE   37   87
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3                37
  MALE                 2                87
D40V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                21 
       TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-7502 
"5Q LOSS WILD-TYPE" 
D40V9, continuous
D40V10, continuous

Clustering(41) Variable = 6P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    7  2
  6P LOSS WILD-TYPE 97 13
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               110 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                13 
$`6P LOSS MUTATED`
TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5882 TCGA-BQ-7056 TCGA-EV-5902 TCGA-G7-6793 
        0.03        10.09        21.63        20.12        19.00        11.05 
TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-7966 
       25.15        14.07         3.68 

$`6P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        7.33        16.37        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.14        26.40        20.58         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
        6.44         1.18         2.10         6.81         0.16        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.37        49.84        26.27        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       34.19        24.89         4.01        51.75        48.62        39.25 
TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       34.82        14.63       194.76         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.03              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            25.15            194.76 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           14.070            13.675 
[1] "0.0 - 25.1 (14.1)"  "0.0 - 194.8 (13.7)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "3.6"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         3        0         5        1
  6P LOSS WILD-TYPE      66       10        25        9
D41V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 3                66
  STAGE II                0                10
  STAGE III               5                25
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  6P LOSS MUTATED    4  0     6
  6P LOSS WILD-TYPE 70 16    33
D41V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                  4                70
  T2                  0                16
  T3+T4               6                33
                   vv
clus                N0 N1 N2
  6P LOSS MUTATED    2  1  1
  6P LOSS WILD-TYPE 24 11  3
D41V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0               2                24
  N1               1                11
  N2               1                 3
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED    5  0  4
  6P LOSS WILD-TYPE 52  6 53
D41V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               5                52
  M1               0                 6
  MX               4                53
D41V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    5  5
  6P LOSS WILD-TYPE 35 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5    5
  6P LOSS WILD-TYPE   35   84
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               5                35
  MALE                 5                84
D41V8, continuous
D41V9, continuous
D41V10, continuous

Clustering(42) Variable = 6Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    9  2
  6Q LOSS WILD-TYPE 95 13
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               11               108 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                13 
$`6Q LOSS MUTATED`
TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 
        0.03        10.09         2.10        86.73        21.63        13.25 
TCGA-BQ-7056 TCGA-EV-5902 TCGA-G7-6793 TCGA-G7-7502 TCGA-GL-7966 
       20.12        19.00        11.05        14.07         3.68 

$`6Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        7.33        16.37        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.14        26.40        20.58         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5876 TCGA-BQ-5877 
        6.44         1.18         6.81         0.16        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.17        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        26.04        25.35        10.88         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.00         7.13         3.78        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        28.80        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 
       51.16        61.02        54.87        34.19        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.75        48.62        39.25        34.82        25.15        14.63 
TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
      194.76         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         4.04         3.68         5.69 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.03              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            86.73            194.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            13.25             13.94 
[1] "0.0 - 86.7 (13.2)"  "0.0 - 194.8 (13.9)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr=" "2"  
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         4        0         6        1
  6Q LOSS WILD-TYPE      65       10        24        9
D42V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 4                65
  STAGE II                0                10
  STAGE III               6                24
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  6Q LOSS MUTATED    4  0     8
  6Q LOSS WILD-TYPE 70 16    31
D42V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                  4                70
  T2                  0                16
  T3+T4               8                31
                   vv
clus                N0 N1 N2
  6Q LOSS MUTATED    3  1  1
  6Q LOSS WILD-TYPE 23 11  3
D42V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0               3                23
  N1               1                11
  N2               1                 3
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED    7  0  3
  6Q LOSS WILD-TYPE 50  6 54
D42V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               7                50
  M1               0                 6
  MX               3                54
D42V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    7  5
  6Q LOSS WILD-TYPE 33 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7    5
  6Q LOSS WILD-TYPE   33   84
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               7                33
  MALE                 5                84
D42V8, continuous
D42V9, continuous
[1] "Remove cluster labels:" "6Q LOSS MUTATED"       
clus
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                 3 
       TCGA-GL-A59T        TCGA-IA-A40U        TCGA-PJ-A5Z9 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
D42V10, continuous

Clustering(43) Variable = 8P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED     3   2
  8P LOSS WILD-TYPE 101  13
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5               114 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                13 
$`8P LOSS MUTATED`
TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 TCGA-DW-5560 
        9.63         7.33        10.09        10.88        11.61 

$`8P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       16.37        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.58         0.46         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 
        1.18         2.10         6.81         0.16        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.84        63.72        22.92        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.13         3.78        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00        24.89         4.01        51.75        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       39.25        34.82        25.15        14.63        14.07       194.76 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
        3.68         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         4.04         3.68         5.69 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             7.33              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            11.61            194.76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           10.090            14.385 
[1] "7.3 - 11.6 (10.1)"  "0.0 - 194.8 (14.4)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr=" "10" 
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         2        1         0        2
  8P LOSS WILD-TYPE      67        9        30        8
D43V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 2                67
  STAGE II                1                 9
  STAGE III               0                30
  STAGE IV                2                 8
                   vv
clus                T1 T2 T3+T4
  8P LOSS MUTATED    2  1     2
  8P LOSS WILD-TYPE 72 15    37
D43V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1                  2                72
  T2                  1                15
  T3+T4               2                37
                   vv
clus                N0 N1 N2
  8P LOSS MUTATED    0  2  0
  8P LOSS WILD-TYPE 26 10  4
D43V5, multiclass
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                40 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846        TCGA-GL-7966 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED    2  2  1
  8P LOSS WILD-TYPE 55  4 56
D43V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               2                55
  M1               2                 4
  MX               1                56
D43V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    3  2
  8P LOSS WILD-TYPE 37 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    2
  8P LOSS WILD-TYPE   37   87
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                37
  MALE                 2                87
D43V8, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                20 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5561        TCGA-DW-7834 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-EV-5901 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D43V9, continuous
D43V10, continuous

Clustering(44) Variable = 8Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     2   1
  8Q LOSS WILD-TYPE 102  14
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               116 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                14 
$`8Q LOSS MUTATED`
TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 
        7.33        10.09        10.88 

$`8Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        53.79        13.55        30.31        25.08        44.61 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       19.56        16.37        11.41        10.98         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.14        26.40        20.58         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
        6.44         1.18         2.10         6.81         0.16        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.37        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        28.80        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       54.87        34.19        19.00        24.89         4.01        51.75 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.07       194.76         3.68         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             7.33              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            10.88            194.76 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           10.090            14.105 
[1] "7.3 - 10.9 (10.1)"  "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr=" "9.5"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         1        1         0        1
  8Q LOSS WILD-TYPE      68        9        30        9
D44V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                68
  STAGE II                1                 9
  STAGE III               0                30
  STAGE IV                1                 9
                   vv
clus                T1 T2 T3+T4
  8Q LOSS MUTATED    1  1     1
  8Q LOSS WILD-TYPE 73 15    38
D44V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1                  1                73
  T2                  1                15
  T3+T4               1                38
                   vv
clus                N0 N1 N2
  8Q LOSS MUTATED    0  1  0
  8Q LOSS WILD-TYPE 26 11  4
D44V5, multiclass
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                41 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BQ-7058        TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-J7-6720 
"8Q LOSS WILD-TYPE" 
                   vv
clus                M0 M1 MX
  8Q LOSS MUTATED    1  1  1
  8Q LOSS WILD-TYPE 56  5 56
D44V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               1                56
  M1               1                 5
  MX               1                56
D44V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  1
  8Q LOSS WILD-TYPE 38 88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    1
  8Q LOSS WILD-TYPE   38   88
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               2                38
  MALE                 1                88
D44V8, continuous
D44V9, continuous
D44V10, continuous

Clustering(45) Variable = 9P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   11  4
  9P LOSS WILD-TYPE 93 11
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               15               104 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                11 
$`9P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5879 
        0.03         0.69         9.63        10.09        20.58        22.92 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7048 TCGA-BQ-7056 TCGA-DZ-6131 TCGA-G7-6793 
       13.25        10.88        93.34        20.12        79.82        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-IA-A40Y 
       34.82        14.63         2.04 

$`9P LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        0.03         0.10         0.03        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        19.56         7.33        16.37 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       11.41        10.98         4.83        50.50        28.14        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.08        15.12         6.44         1.18         2.10 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.81         0.16        86.73        19.23         8.84        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76       123.58        48.26        96.92        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.37        49.84        26.27        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       28.80        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       19.00        24.89         4.01        51.75        48.62        39.25 
TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       25.15        14.07       194.76         3.68         7.73         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        5.85         2.99         4.57        14.14         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.03              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            93.34            194.76 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           13.250            13.905 
[1] "0.0 - 93.3 (13.2)"  "0.0 - 194.8 (13.9)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         4        0         7        4
  9P LOSS WILD-TYPE      65       10        23        6
D45V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 4                65
  STAGE II                0                10
  STAGE III               7                23
  STAGE IV                4                 6
                   vv
clus                T1 T2 T3+T4
  9P LOSS MUTATED    4  2    11
  9P LOSS WILD-TYPE 70 14    28
D45V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  4                70
  T2                  2                14
  T3+T4              11                28
                   vv
clus                N0 N1 N2
  9P LOSS MUTATED    5  5  1
  9P LOSS WILD-TYPE 21  7  3
D45V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               5                21
  N1               5                 7
  N2               1                 3
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED    6  3  6
  9P LOSS WILD-TYPE 51  3 51
D45V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               6                51
  M1               3                 3
  MX               6                51
D45V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   10  7
  9P LOSS WILD-TYPE 30 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10    7
  9P LOSS WILD-TYPE   30   82
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              10                30
  MALE                 7                82
D45V8, continuous
D45V9, continuous
D45V10, continuous

Clustering(46) Variable = 9Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   13  4
  9Q LOSS WILD-TYPE 91 11
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               17               102 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                11 
$`9Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-A44B 
        0.03         0.69         9.63        10.09        10.98         2.10 
TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7048 TCGA-BQ-7055 TCGA-BQ-7056 
       22.92        13.25        10.88        93.34        26.27        20.12 
TCGA-DZ-6131 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-IA-A40Y 
       79.82        11.05        34.82        14.63         2.04 

$`9Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        0.03         0.10         0.03        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        19.56         7.33        16.37 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       11.41         4.83        50.50        28.14        26.40        20.58 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
        0.46         1.08        15.12         6.44         1.18         6.81 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
        0.16        86.73        19.23         8.84        63.72        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.58        48.26        96.92        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       49.84        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        28.80        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        34.19        19.00        24.89 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
        4.01        51.75        48.62        39.25        25.15        14.07 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.76         3.68         7.73         1.05         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.57        14.14         1.08         4.04         3.68         5.69 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.03              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            93.34            194.76 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           11.050            14.105 
[1] "0.0 - 93.3 (11.1)"  "0.0 - 194.8 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         5        1         8        3
  9Q LOSS WILD-TYPE      64        9        22        7
D46V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 5                64
  STAGE II                1                 9
  STAGE III               8                22
  STAGE IV                3                 7
                   vv
clus                T1 T2 T3+T4
  9Q LOSS MUTATED    5  1    12
  9Q LOSS WILD-TYPE 69 15    27
D46V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  5                69
  T2                  1                15
  T3+T4              12                27
                   vv
clus                N0 N1 N2
  9Q LOSS MUTATED    4  5  1
  9Q LOSS WILD-TYPE 22  7  3
D46V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0               4                22
  N1               5                 7
  N2               1                 3
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED    8  2  6
  9Q LOSS WILD-TYPE 49  4 51
D46V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               8                49
  M1               2                 4
  MX               6                51
D46V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    9  9
  9Q LOSS WILD-TYPE 31 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9    9
  9Q LOSS WILD-TYPE   31   80
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               9                31
  MALE                 9                80
D46V8, continuous
D46V9, continuous
[1] "Remove cluster labels:" "9Q LOSS MUTATED"       
clus
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 3 
       TCGA-GL-A59T        TCGA-IA-A40U        TCGA-PJ-A5Z9 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
D46V10, continuous

Clustering(47) Variable = 10P LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    7  1
  10P LOSS WILD-TYPE 97 14
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                111 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                 14 
$`10P LOSS MUTATED`
TCGA-AL-3466 TCGA-B9-4116 TCGA-B9-A44B TCGA-BQ-5876 TCGA-DZ-6131 TCGA-G7-7501 
        9.63        20.58         2.10        19.23        79.82        14.63 
TCGA-G7-7502 TCGA-GL-7966 
       14.07         3.68 

$`10P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.14        26.40         0.46         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5877 
        6.44         1.18         6.81         0.16        86.73         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.17        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       28.80        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00        24.89         4.01        51.75        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM 
       39.25        34.82        25.15       194.76         7.73         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        5.85         2.99         4.57        14.14         2.04         1.08 
TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.04         3.68         5.69 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              2.10               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             79.82             194.76 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.35              13.61 
[1] "2.1 - 79.8 (14.4)"  "0.0 - 194.8 (13.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D47V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         2        0         4        1
  10P LOSS WILD-TYPE      67       10        26        9
D47V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  2                 67
  STAGE II                 0                 10
  STAGE III                4                 26
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  10P LOSS MUTATED    2  1     5
  10P LOSS WILD-TYPE 72 15    34
D47V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                   2                 72
  T2                   1                 15
  T3+T4                5                 34
                    vv
clus                 N0 N1 N2
  10P LOSS MUTATED    1  3  0
  10P LOSS WILD-TYPE 25  9  4
D47V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                1                 25
  N1                3                  9
  N2                0                  4
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED    1  1  4
  10P LOSS WILD-TYPE 56  5 53
D47V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                1                 56
  M1                1                  5
  MX                4                 53
D47V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3  5
  10P LOSS WILD-TYPE 37 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3    5
  10P LOSS WILD-TYPE   37   84
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                3                 37
  MALE                  5                 84
D47V8, continuous
D47V9, continuous
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                  3 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-PJ-A5Z9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
D47V10, continuous

Clustering(48) Variable = 10Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    6  2
  10Q LOSS WILD-TYPE 98 13
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                111 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                 13 
$`10Q LOSS MUTATED`
TCGA-AL-3466 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 TCGA-G7-7501 
        9.63         2.10        19.23        21.63        79.82        14.63 
TCGA-G7-7502 TCGA-GL-7966 
       14.07         3.68 

$`10Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 
        0.69         0.72         0.03         0.10         0.03        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
       15.12         6.44         1.18         6.81         0.16        86.73 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.84        63.72        22.92        43.17        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       28.80        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00        24.89         4.01        51.75        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM 
       39.25        34.82        25.15       194.76         7.73         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
        5.85         2.99         4.57        14.14         2.04         1.08 
TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.04         3.68         5.69 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2.10               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             79.82             194.76 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             14.35              13.61 
[1] "2.1 - 79.8 (14.4)"  "0.0 - 194.8 (13.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr=" "2.5"
D48V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         2        0         5        1
  10Q LOSS WILD-TYPE      67       10        25        9
D48V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  2                 67
  STAGE II                 0                 10
  STAGE III                5                 25
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  10Q LOSS MUTATED    2  0     6
  10Q LOSS WILD-TYPE 72 16    33
D48V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                   2                 72
  T2                   0                 16
  T3+T4                6                 33
                    vv
clus                 N0 N1 N2
  10Q LOSS MUTATED    2  3  0
  10Q LOSS WILD-TYPE 24  9  4
D48V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                2                 24
  N1                3                  9
  N2                0                  4
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED    2  1  4
  10Q LOSS WILD-TYPE 55  5 53
D48V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                2                 55
  M1                1                  5
  MX                4                 53
D48V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    2  6
  10Q LOSS WILD-TYPE 38 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2    6
  10Q LOSS WILD-TYPE   38   83
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                2                 38
  MALE                  6                 83
D48V8, continuous
D48V9, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  3 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-PJ-A5Z9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D48V10, continuous

Clustering(49) Variable = 11P LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    6  2
  11P LOSS WILD-TYPE 98 13
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                111 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 13 
$`11P LOSS MUTATED`
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 
        0.69         7.33        10.98        19.23         8.84        21.63 
TCGA-G7-7502 TCGA-IA-A40Y 
       14.07         2.04 

$`11P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       16.37        10.09        11.41         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.58         0.46         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5878 
        1.18         2.10         6.81         0.16        86.73        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.17        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.74         3.75        14.63         3.02        28.80        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        34.19        19.00 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       24.89         4.01        51.75        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       34.82        25.15        14.63       194.76         3.68         7.73 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
        1.05         5.85         2.99         4.57        14.14         1.08 
TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.04         3.68         5.69 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.69               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             21.63             194.76 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              9.91              14.14 
[1] "0.7 - 21.6 (9.9)"   "0.0 - 194.8 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "6"  
D49V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         3        2         3        1
  11P LOSS WILD-TYPE      66        8        27        9
D49V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  3                 66
  STAGE II                 2                  8
  STAGE III                3                 27
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  11P LOSS MUTATED    3  2     4
  11P LOSS WILD-TYPE 71 14    35
D49V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   3                 71
  T2                   2                 14
  T3+T4                4                 35
                    vv
clus                 N0 N1 N2
  11P LOSS MUTATED    1  2  0
  11P LOSS WILD-TYPE 25 10  4
D49V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                1                 25
  N1                2                 10
  N2                0                  4
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED    4  1  4
  11P LOSS WILD-TYPE 53  5 53
D49V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                4                 53
  M1                1                  5
  MX                4                 53
D49V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    4  5
  11P LOSS WILD-TYPE 36 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    5
  11P LOSS WILD-TYPE   36   84
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                4                 36
  MALE                  5                 84
D49V8, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 21 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6793 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D49V9, continuous
D49V10, continuous

Clustering(50) Variable = 11Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    7  4
  11Q LOSS WILD-TYPE 97 11
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                11                108 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 11 
$`11Q LOSS MUTATED`
TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5889 
        7.33         2.10        19.23         8.84        21.63        10.88 
TCGA-BQ-5890 TCGA-BQ-7044 TCGA-G7-6793 TCGA-G7-7502 TCGA-IA-A40Y 
        7.63       123.58        11.05        14.07         2.04 

$`11Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 
        0.69         0.72         0.03         0.10         0.03         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        53.79        13.55        30.31        25.08        44.61 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       19.56        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 
       15.12         6.44         1.18         6.81         0.16        86.73 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.17        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 
       30.28        26.04        25.35        13.25         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.89         2.76        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        28.80        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        34.19        19.00        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.75        48.62        39.25        34.82        25.15        14.63 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.76         3.68         7.73         1.05         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.57        14.14         1.08         4.04         3.68         5.69 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              2.04               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            123.58             194.76 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            10.880             14.385 
[1] "2.0 - 123.6 (10.9)" "0.0 - 194.8 (14.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "5.6"
D50V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         2        1         6        3
  11Q LOSS WILD-TYPE      67        9        24        7
D50V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  2                 67
  STAGE II                 1                  9
  STAGE III                6                 24
  STAGE IV                 3                  7
                    vv
clus                 T1 T2 T3+T4
  11Q LOSS MUTATED    2  1     9
  11Q LOSS WILD-TYPE 72 15    30
D50V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   2                 72
  T2                   1                 15
  T3+T4                9                 30
                    vv
clus                 N0 N1 N2
  11Q LOSS MUTATED    2  3  1
  11Q LOSS WILD-TYPE 24  9  3
D50V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                2                 24
  N1                3                  9
  N2                1                  3
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED    5  2  4
  11Q LOSS WILD-TYPE 52  4 53
D50V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                5                 52
  M1                2                  4
  MX                4                 53
D50V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    4  8
  11Q LOSS WILD-TYPE 36 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    8
  11Q LOSS WILD-TYPE   36   81
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                4                 36
  MALE                  8                 81
D50V8, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6796 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D50V9, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  3 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-PJ-A5Z9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D50V10, continuous

Clustering(51) Variable = 13Q LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    8  3
  13Q LOSS WILD-TYPE 96 12
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                11                108 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 12 
$`13Q LOSS MUTATED`
TCGA-A4-7287 TCGA-A4-7915 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5879 TCGA-BQ-5882 
        0.69         0.23        10.09        86.73        22.92        21.63 
TCGA-BQ-5894 TCGA-G7-6793 TCGA-G7-7502 TCGA-GL-7966 TCGA-IA-A40Y 
        2.76        11.05        14.07         3.68         2.04 

$`13Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        19.56         7.33 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       16.37        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.58         0.46         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5876 TCGA-BQ-5877 
        1.18         2.10         6.81         0.16        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        43.17        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.89       123.58        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.37        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.00         7.13         3.78        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        28.80        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        34.19        19.00        24.89 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        51.75        48.62        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       14.63       194.76         7.73         1.05         5.85         2.99 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.57        14.14         1.08         4.04         3.68         5.69 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.23               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             86.73             194.76 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            10.090             14.385 
[1] "0.2 - 86.7 (10.1)"  "0.0 - 194.8 (14.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "3.9"
D51V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         3        1         5        2
  13Q LOSS WILD-TYPE      66        9        25        8
D51V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  3                 66
  STAGE II                 1                  9
  STAGE III                5                 25
  STAGE IV                 2                  8
                    vv
clus                 T1 T2 T3+T4
  13Q LOSS MUTATED    3  1     7
  13Q LOSS WILD-TYPE 71 15    32
D51V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                   3                 71
  T2                   1                 15
  T3+T4                7                 32
                    vv
clus                 N0 N1 N2
  13Q LOSS MUTATED    2  4  1
  13Q LOSS WILD-TYPE 24  8  3
D51V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                2                 24
  N1                4                  8
  N2                1                  3
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED    4  1  6
  13Q LOSS WILD-TYPE 53  5 51
D51V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                4                 53
  M1                1                  5
  MX                6                 51
D51V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    8  3
  13Q LOSS WILD-TYPE 32 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8    3
  13Q LOSS WILD-TYPE   32   86
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                8                 32
  MALE                  3                 86
D51V8, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6796 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D51V9, continuous
D51V10, continuous

Clustering(52) Variable = 14Q LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   23  3
  14Q LOSS WILD-TYPE 81 12
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                26                 93 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                 12 
$`14Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3473 
        0.03         0.69         0.10         4.60         9.63        25.08 
TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 
       44.61         7.33        10.09        20.58         6.81        19.23 
TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-DZ-6132 
       30.28        13.25        10.88         2.76        79.82        80.84 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-8500 TCGA-IA-A40U 
       11.05        34.82        14.63        14.07         7.73         4.57 
TCGA-IA-A40Y TCGA-PJ-A5Z8 
        2.04         3.68 

$`14Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       15.95        35.18         0.03         0.89         0.23         1.61 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
        0.03         0.07         0.69         0.72         0.03         0.10 
TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B1-5398 
        0.03        58.45        53.79        13.55        30.31        19.56 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       16.37        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40         0.46         1.08        15.12         6.44         1.18 
TCGA-B9-A44B TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        2.10         0.16        86.73         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
       43.17        47.80        21.63        40.83        26.04        26.04 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 
       25.35         7.63         0.95        11.97         7.89       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       28.80        51.16        61.02        54.87        34.19        19.00 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
       24.89         4.01        51.75        48.62        39.25        25.15 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40X 
      194.76         3.68         1.05         5.85         2.99        14.14 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z9 
        1.08         4.04         5.69 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.03               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             80.84             194.76 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            10.485             15.120 
[1] "0.0 - 80.8 (10.5)"  "0.0 - 194.8 (15.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D52V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        11        3         6        5
  14Q LOSS WILD-TYPE      58        7        24        5
D52V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 11                 58
  STAGE II                 3                  7
  STAGE III                6                 24
  STAGE IV                 5                  5
                    vv
clus                 T1 T2 T3+T4
  14Q LOSS MUTATED   11  4    12
  14Q LOSS WILD-TYPE 63 12    27
D52V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                  11                 63
  T2                   4                 12
  T3+T4               12                 27
                    vv
clus                 N0 N1 N2
  14Q LOSS MUTATED    6  5  2
  14Q LOSS WILD-TYPE 20  7  2
D52V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                6                 20
  N1                5                  7
  N2                2                  2
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED   10  3 12
  14Q LOSS WILD-TYPE 47  3 45
D52V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               10                 47
  M1                3                  3
  MX               12                 45
D52V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   11 16
  14Q LOSS WILD-TYPE 29 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11   16
  14Q LOSS WILD-TYPE   29   73
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               11                 29
  MALE                 16                 73
D52V8, continuous
D52V9, continuous
[1] "Remove cluster labels:" "14Q LOSS MUTATED"      
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  3 
        TCGA-B9-A44B         TCGA-GL-A59T         TCGA-PJ-A5Z9 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
D52V10, continuous
[1] "Remove cluster labels:" "14Q LOSS MUTATED"       "14Q LOSS WILD-TYPE"    
clus
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  2 
named character(0)

Clustering(53) Variable = 15Q LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   10  3
  15Q LOSS WILD-TYPE 94 12
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                13                106 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                 12 
$`15Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5879 
        0.03         0.10        19.56        10.09         6.81        22.92 
TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-7966 
       21.63        10.88         2.76        34.82        14.07         3.68 
TCGA-PJ-A5Z8 
        3.68 

$`15Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 
       13.55        30.31        25.08        44.61         7.33        16.37 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       11.41        10.98         4.83        50.50        28.14        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.58         0.46         1.08        15.12         6.44         1.18 
TCGA-B9-A44B TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        2.10         0.16        86.73        19.23         8.84        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.17        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25         7.63         0.95        11.97         7.89 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.37        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        28.80        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       54.87        34.19        19.00        24.89         4.01        51.75 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-6846 
       48.62        11.05        39.25        25.15        14.63       194.76 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X 
        7.73         1.05         5.85         2.99         4.57        14.14 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z9 
        2.04         1.08         4.04         5.69 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.03               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             34.82             194.76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            10.090             14.385 
[1] "0.0 - 34.8 (10.1)"  "0.0 - 194.8 (14.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
[1] "hr=" "5.8"
D53V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         5        1         5        2
  15Q LOSS WILD-TYPE      64        9        25        8
D53V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  5                 64
  STAGE II                 1                  9
  STAGE III                5                 25
  STAGE IV                 2                  8
                    vv
clus                 T1 T2 T3+T4
  15Q LOSS MUTATED    5  1     8
  15Q LOSS WILD-TYPE 69 15    31
D53V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                   5                 69
  T2                   1                 15
  T3+T4                8                 31
                    vv
clus                 N0 N1 N2
  15Q LOSS MUTATED    3  4  0
  15Q LOSS WILD-TYPE 23  8  4
D53V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                3                 23
  N1                4                  8
  N2                0                  4
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED    8  2  3
  15Q LOSS WILD-TYPE 49  4 54
D53V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                8                 49
  M1                2                  4
  MX                3                 54
D53V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    5  9
  15Q LOSS WILD-TYPE 35 80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    9
  15Q LOSS WILD-TYPE   35   80
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                5                 35
  MALE                  9                 80
D53V8, continuous
D53V9, continuous
D53V10, continuous

Clustering(54) Variable = 16P LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     1   2
  16P LOSS WILD-TYPE 103  13
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                116 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 13 
$`16P LOSS MUTATED`
TCGA-A4-7287 TCGA-BQ-5882 TCGA-G7-6793 
        0.69        21.63        11.05 

$`16P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12         6.44         1.18         2.10         6.81         0.16 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        28.80        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        34.19        19.00        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.75        48.62        39.25        34.82        25.15        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.07       194.76         3.68         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.69               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             21.63             194.76 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            11.050             13.905 
[1] "0.7 - 21.6 (11.1)"  "0.0 - 194.8 (13.9)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "13" 
D54V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         1        0         2        1
  16P LOSS WILD-TYPE      68       10        28        9
D54V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  1                 68
  STAGE II                 0                 10
  STAGE III                2                 28
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  16P LOSS MUTATED    1  0     3
  16P LOSS WILD-TYPE 73 16    36
D54V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                   1                 73
  T2                   0                 16
  T3+T4                3                 36
                    vv
clus                 N0 N1 N2
  16P LOSS MUTATED    1  0  1
  16P LOSS WILD-TYPE 25 12  3
D54V5, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 40 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-AL-3466         TCGA-AL-3472 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5885 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6795 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-GL-6846         TCGA-GL-7966 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A59R         TCGA-IA-A40U         TCGA-IA-A40Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-J7-6720 
"16P LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED    2  0  2
  16P LOSS WILD-TYPE 55  6 55
D54V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                2                 55
  M1                0                  6
  MX                2                 55
D54V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    3  1
  16P LOSS WILD-TYPE 37 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    1
  16P LOSS WILD-TYPE   37   88
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 37
  MALE                  1                 88
D54V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 21 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6796 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D54V9, continuous
D54V10, continuous

Clustering(55) Variable = 16Q LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     1   2
  16Q LOSS WILD-TYPE 103  13
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                116 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 13 
$`16Q LOSS MUTATED`
TCGA-A4-7287 TCGA-BQ-5882 TCGA-G7-6793 
        0.69        21.63        11.05 

$`16Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 
        0.72         0.03         0.10         0.03         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        19.56 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33        16.37        10.09        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12         6.44         1.18         2.10         6.81         0.16 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        28.80        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        34.19        19.00        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.75        48.62        39.25        34.82        25.15        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       14.07       194.76         3.68         7.73         1.05         5.85 
TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        2.99         4.57        14.14         2.04         1.08         4.04 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3.68         5.69 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.69               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             21.63             194.76 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            11.050             13.905 
[1] "0.7 - 21.6 (11.1)"  "0.0 - 194.8 (13.9)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "13" 
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         1        0         2        1
  16Q LOSS WILD-TYPE      68       10        28        9
D55V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  1                 68
  STAGE II                 0                 10
  STAGE III                2                 28
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  16Q LOSS MUTATED    1  0     3
  16Q LOSS WILD-TYPE 73 16    36
D55V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                   1                 73
  T2                   0                 16
  T3+T4                3                 36
                    vv
clus                 N0 N1 N2
  16Q LOSS MUTATED    1  0  1
  16Q LOSS WILD-TYPE 25 12  3
D55V5, multiclass
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 40 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-AL-3466         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5885 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DW-7963 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6795 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-A59R         TCGA-IA-A40U         TCGA-IA-A40Y 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-J7-6720 
"16Q LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED    2  0  2
  16Q LOSS WILD-TYPE 55  6 55
D55V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                2                 55
  M1                0                  6
  MX                2                 55
D55V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  1
  16Q LOSS WILD-TYPE 37 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    1
  16Q LOSS WILD-TYPE   37   88
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 37
  MALE                  1                 88
D55V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 21 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6796 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D55V9, continuous
D55V10, continuous

Clustering(56) Variable = 17P LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED     2   3
  17P LOSS WILD-TYPE 102  12
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                114 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 12 
$`17P LOSS MUTATED`
TCGA-A4-7287 TCGA-A4-7915 TCGA-AL-3466 TCGA-BQ-7058 TCGA-G7-6793 
        0.69         0.23         9.63        11.28        11.05 

$`17P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        0.03         0.10         0.03        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        19.56         7.33        16.37 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.58         0.46         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 
        1.18         2.10         6.81         0.16        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.84        63.72        22.92        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
       50.37        49.84        26.27        20.12         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       28.80        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       34.19        19.00        24.89         4.01        51.75        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       39.25        34.82        25.15        14.63        14.07       194.76 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
        3.68         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         2.04         1.08         4.04         3.68         5.69 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             11.28             194.76 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             9.630             14.385 
[1] "0.2 - 11.3 (9.6)"   "0.0 - 194.8 (14.4)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "23" 
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         1        1         2        3
  17P LOSS WILD-TYPE      68        9        28        7
D56V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  1                 68
  STAGE II                 1                  9
  STAGE III                2                 28
  STAGE IV                 3                  7
                    vv
clus                 T1 T2 T3+T4
  17P LOSS MUTATED    1  2     4
  17P LOSS WILD-TYPE 73 14    35
D56V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   1                 73
  T2                   2                 14
  T3+T4                4                 35
                    vv
clus                 N0 N1 N2
  17P LOSS MUTATED    2  1  2
  17P LOSS WILD-TYPE 24 11  2
D56V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                2                 24
  N1                1                 11
  N2                2                  2
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED    2  2  3
  17P LOSS WILD-TYPE 55  4 54
D56V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                2                 55
  M1                2                  4
  MX                3                 54
D56V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    4  3
  17P LOSS WILD-TYPE 36 86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4    3
  17P LOSS WILD-TYPE   36   86
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                4                 36
  MALE                  3                 86
D56V8, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-DW-5560 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6796         TCGA-G7-6797 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
D56V9, continuous
D56V10, continuous

Clustering(57) Variable = 18P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   14  4
  18P LOSS WILD-TYPE 90 11
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                18                101 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 11 
$`18P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-8310 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 
        0.03         0.03         7.33        10.09        20.58         8.84 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       22.92        21.63        25.35         2.76       123.58        93.34 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-DW-7840 TCGA-EV-5903 TCGA-GL-7966 TCGA-IA-A40Y 
       11.28         7.63         3.75        24.89         3.68         2.04 

$`18P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        0.23         1.61         4.60         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        19.56        16.37 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       11.41        10.98         4.83        50.50        28.14        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.08        15.12         6.44         1.18         2.10 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
        6.81         0.16        86.73        19.23        63.72        43.17 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       47.80        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 
       10.88         7.63         0.95        11.97         7.89        48.26 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       20.12         7.00         7.13         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 
      129.86        35.93        37.55        24.46        13.74        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        28.80        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       54.87        34.19        19.00         4.01        51.75        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        14.63        14.07 
TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
      194.76         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         1.08         4.04         3.68         5.69 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.03               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            123.58             194.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             9.465             14.140 
[1] "0.0 - 123.6 (9.5)"  "0.0 - 194.8 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         5        1         9        3
  18P LOSS WILD-TYPE      64        9        21        7
D57V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  5                 64
  STAGE II                 1                  9
  STAGE III                9                 21
  STAGE IV                 3                  7
                    vv
clus                 T1 T2 T3+T4
  18P LOSS MUTATED    5  3    12
  18P LOSS WILD-TYPE 69 13    27
D57V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                   5                 69
  T2                   3                 13
  T3+T4               12                 27
                    vv
clus                 N0 N1 N2
  18P LOSS MUTATED    4  5  1
  18P LOSS WILD-TYPE 22  7  3
D57V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                4                 22
  N1                5                  7
  N2                1                  3
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED    9  3  6
  18P LOSS WILD-TYPE 48  3 51
D57V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                9                 48
  M1                3                  3
  MX                6                 51
D57V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    6 14
  18P LOSS WILD-TYPE 34 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6   14
  18P LOSS WILD-TYPE   34   75
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                6                 34
  MALE                 14                 75
D57V8, continuous
D57V9, continuous
D57V10, continuous

Clustering(58) Variable = 18Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   14  4
  18Q LOSS WILD-TYPE 90 11
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                101 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 11 
$`18Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-8310 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 
        0.03         0.03         7.33        10.09        20.58         8.84 
TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       22.92        21.63        25.35         2.76       123.58        93.34 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-DW-7840 TCGA-EV-5903 TCGA-GL-7966 TCGA-IA-A40Y 
       11.28         7.63         3.75        24.89         3.68         2.04 

$`18Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        0.23         1.61         4.60         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        19.56        16.37 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       11.41        10.98         4.83        50.50        28.14        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.08        15.12         6.44         1.18         2.10 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
        6.81         0.16        86.73        19.23        63.72        43.17 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       47.80        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 
       10.88         7.63         0.95        11.97         7.89        48.26 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       20.12         7.00         7.13         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 
      129.86        35.93        37.55        24.46        13.74        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        28.80        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       54.87        34.19        19.00         4.01        51.75        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        14.63        14.07 
TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U 
      194.76         7.73         1.05         5.85         2.99         4.57 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       14.14         1.08         4.04         3.68         5.69 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.03               0.03 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            123.58             194.76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             9.465             14.140 
[1] "0.0 - 123.6 (9.5)"  "0.0 - 194.8 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         5        1        10        3
  18Q LOSS WILD-TYPE      64        9        20        7
D58V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  5                 64
  STAGE II                 1                  9
  STAGE III               10                 20
  STAGE IV                 3                  7
                    vv
clus                 T1 T2 T3+T4
  18Q LOSS MUTATED    5  3    13
  18Q LOSS WILD-TYPE 69 13    26
D58V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                   5                 69
  T2                   3                 13
  T3+T4               13                 26
                    vv
clus                 N0 N1 N2
  18Q LOSS MUTATED    4  5  1
  18Q LOSS WILD-TYPE 22  7  3
D58V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                4                 22
  N1                5                  7
  N2                1                  3
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   10  3  6
  18Q LOSS WILD-TYPE 47  3 51
D58V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               10                 47
  M1                3                  3
  MX                6                 51
D58V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    7 14
  18Q LOSS WILD-TYPE 33 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7   14
  18Q LOSS WILD-TYPE   33   75
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                7                 33
  MALE                 14                 75
D58V8, continuous
D58V9, continuous
D58V10, continuous

Clustering(59) Variable = 19P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    8  0
  19P LOSS WILD-TYPE 96 15
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                111 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                 15 
$`19P LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-8310 TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5891 
        0.03         0.03         7.33         2.10        19.23         0.95 
TCGA-G7-7502 TCGA-IA-A40Y 
       14.07         2.04 

$`19P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        0.23         1.61         4.60         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        19.56        16.37 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.58         0.46         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
        1.18         6.81         0.16        86.73         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.74         3.75        14.63         3.02        28.80        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        34.19        19.00 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       24.89         4.01        51.75        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       34.82        25.15        14.63       194.76         3.68         7.73 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
        1.05         5.85         2.99         4.57        14.14         1.08 
TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        4.04         3.68         5.69 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.03               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             19.23             194.76 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2.07              14.63 
[1] "0.0 - 19.2 (2.1)"   "0.0 - 194.8 (14.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr="     "9300000"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         2        1         4        1
  19P LOSS WILD-TYPE      67        9        26        9
D59V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  2                 67
  STAGE II                 1                  9
  STAGE III                4                 26
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  19P LOSS MUTATED    2  2     5
  19P LOSS WILD-TYPE 72 14    34
D59V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                   2                 72
  T2                   2                 14
  T3+T4                5                 34
                    vv
clus                 N0 N1 N2
  19P LOSS MUTATED    2  1  0
  19P LOSS WILD-TYPE 24 11  4
D59V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                2                 24
  N1                1                 11
  N2                0                  4
                    vv
clus                 M0 M1 MX
  19P LOSS MUTATED    2  1  4
  19P LOSS WILD-TYPE 55  5 53
D59V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                2                 55
  M1                1                  5
  MX                4                 53
D59V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3  6
  19P LOSS WILD-TYPE 37 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    6
  19P LOSS WILD-TYPE   37   83
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                 37
  MALE                  6                 83
D59V8, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7828         TCGA-AL-3466         TCGA-DW-5560 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D59V9, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                  3 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-PJ-A5Z9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D59V10, continuous

Clustering(60) Variable = 19Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    7  0
  19Q LOSS WILD-TYPE 97 15
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                112 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                 15 
$`19Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-8310 TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5891 TCGA-G7-7502 
        0.03         0.03         7.33         2.10         0.95        14.07 
TCGA-IA-A40Y 
        2.04 

$`19Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        0.23         1.61         4.60         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.03         0.10         0.03         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        19.56        16.37 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        11.41        10.98         4.83        50.50        28.14 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.58         0.46         1.08        15.12         6.44 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        1.18         6.81         0.16        86.73        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.17        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.63        11.97         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00        24.89         4.01        51.75        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7966 
       39.25        34.82        25.15        14.63       194.76         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X 
        7.73         1.05         5.85         2.99         4.57        14.14 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        1.08         4.04         3.68         5.69 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.03               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             14.07             194.76 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              2.04              14.63 
[1] "0.0 - 14.1 (2.0)"   "0.0 - 194.8 (14.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr="     "3400000"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         1        1         4        1
  19Q LOSS WILD-TYPE      68        9        26        9
D60V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                 68
  STAGE II                 1                  9
  STAGE III                4                 26
  STAGE IV                 1                  9
                    vv
clus                 T1 T2 T3+T4
  19Q LOSS MUTATED    1  2     5
  19Q LOSS WILD-TYPE 73 14    34
D60V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                   1                 73
  T2                   2                 14
  T3+T4                5                 34
                    vv
clus                 N0 N1 N2
  19Q LOSS MUTATED    2  1  0
  19Q LOSS WILD-TYPE 24 11  4
D60V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                2                 24
  N1                1                 11
  N2                0                  4
                    vv
clus                 M0 M1 MX
  19Q LOSS MUTATED    1  1  4
  19Q LOSS WILD-TYPE 56  5 53
D60V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                1                 56
  M1                1                  5
  MX                4                 53
D60V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  5
  19Q LOSS WILD-TYPE 37 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    5
  19Q LOSS WILD-TYPE   37   84
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 37
  MALE                  5                 84
D60V8, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7828         TCGA-AL-3466         TCGA-DW-5560 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D60V9, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                  3 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-PJ-A5Z9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D60V10, continuous

Clustering(61) Variable = 21Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   19  1
  21Q LOSS WILD-TYPE 85 14
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                20                 99 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 14 
$`21Q LOSS MUTATED`
TCGA-A4-7288 TCGA-A4-8516 TCGA-AL-3468 TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-4114 
       15.95         0.72        53.79        16.37        10.09        28.14 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 
        2.10         6.81        86.73        30.28        10.88         7.63 
TCGA-BQ-5894 TCGA-BQ-7061 TCGA-DZ-6134 TCGA-G7-6796 TCGA-GL-7966 TCGA-IA-A40U 
        2.76         7.13        61.02        34.82         3.68         4.57 
TCGA-IA-A40Y TCGA-PJ-A5Z9 
        2.04         5.69 

$`21Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03         0.69         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
        0.23         1.61         4.60         0.03         0.07         0.69 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
        0.03         0.10         0.03         9.63        58.45        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-4103 
       30.31        25.08        44.61        19.56         7.33        11.41 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.98         4.83        50.50        26.40        20.58         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5876 
        1.08        15.12         6.44         1.18         0.16        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.84        63.72        22.92        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
       40.83        26.04        26.04        25.35        13.25         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.89       123.58        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.37        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       11.28         7.63         7.00         3.78        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        28.80        79.82        80.84        51.16 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       54.87        34.19        19.00        24.89         4.01        51.75 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        39.25        25.15        14.63        14.07 
TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40X 
      194.76         7.73         1.05         5.85         2.99        14.14 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 
        1.08         4.04         3.68 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.72               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             86.73             194.76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              8.86              14.14 
[1] "0.7 - 86.7 (8.9)"   "0.0 - 194.8 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
[1] "hr=" "2.2"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         6        2        10        3
  21Q LOSS WILD-TYPE      63        8        20        7
D61V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  6                 63
  STAGE II                 2                  8
  STAGE III               10                 20
  STAGE IV                 3                  7
                    vv
clus                 T1 T2 T3+T4
  21Q LOSS MUTATED    7  4    12
  21Q LOSS WILD-TYPE 67 12    27
D61V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                   7                 67
  T2                   4                 12
  T3+T4               12                 27
                    vv
clus                 N0 N1 N2
  21Q LOSS MUTATED    4  4  0
  21Q LOSS WILD-TYPE 22  8  4
D61V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                4                 22
  N1                4                  8
  N2                0                  4
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED    9  3  9
  21Q LOSS WILD-TYPE 48  3 48
D61V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                9                 48
  M1                3                  3
  MX                9                 48
D61V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    9 14
  21Q LOSS WILD-TYPE 31 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      9   14
  21Q LOSS WILD-TYPE   31   75
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                9                 31
  MALE                 14                 75
D61V8, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 21 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6793 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D61V9, continuous
[1] "Remove cluster labels:" "21Q LOSS WILD-TYPE"    
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                  1 
      TCGA-B9-A44B       TCGA-IA-A40U       TCGA-PJ-A5Z9 
"21Q LOSS MUTATED" "21Q LOSS MUTATED" "21Q LOSS MUTATED" 
D61V10, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"       "21Q LOSS WILD-TYPE"    
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  1 
named character(0)

Clustering(62) Variable = 22Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   27  4
  22Q LOSS WILD-TYPE 77 11
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                 88 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 11 
$`22Q LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3925 
        0.03        15.95         4.60         9.63         7.33        16.37 
TCGA-B3-3926 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5879 
       10.09         2.10         6.81        86.73         8.84        22.92 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 
       26.04        30.28         7.63         0.95         2.76       123.58 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 
       61.28        50.37        26.27        20.12         7.13        79.82 
TCGA-EV-5902 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 
       19.00        11.05        25.15        14.63        14.07         3.68 
TCGA-IA-A40Y 
        2.04 

$`22Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.69         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
        1.61         0.03         0.07         0.69         0.72         0.03 
TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        0.10         0.03        58.45        53.79        13.55        30.31 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       25.08        44.61        19.56        11.41        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5876 TCGA-BQ-5878 
       15.12         6.44         1.18         0.16        19.23        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5886 TCGA-BQ-5887 
       43.17        47.80        21.63        40.83        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 
       13.25        10.88        11.97         7.89        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        44.84        49.84        11.28         7.63         7.00 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.74         3.75        14.63         3.02        28.80 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       80.84        51.16        61.02        54.87        34.19        24.89 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-6846 
        4.01        51.75        48.62        39.25        34.82       194.76 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X 
        7.73         1.05         5.85         2.99         4.57        14.14 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        1.08         4.04         3.68         5.69 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.03               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            123.58             194.76 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            14.070             13.675 
[1] "0.0 - 123.6 (14.1)" "0.0 - 194.8 (13.7)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8515         TCGA-A4-8516         TCGA-A4-8517 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-A48D         TCGA-AL-3466 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A5W8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-B9-A5W9         TCGA-BQ-5875         TCGA-BQ-5876 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-DZ-6131 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7966 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-GL-8500         TCGA-GL-A4EM         TCGA-GL-A59R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-IA-A40X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-IZ-8195         TCGA-IZ-8196 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z8         TCGA-PJ-A5Z9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         8        3        14        4
  22Q LOSS WILD-TYPE      61        7        16        6
D62V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  8                 61
  STAGE II                 3                  7
  STAGE III               14                 16
  STAGE IV                 4                  6
                    vv
clus                 T1 T2 T3+T4
  22Q LOSS MUTATED   10  3    18
  22Q LOSS WILD-TYPE 64 13    21
D62V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                  10                 64
  T2                   3                 13
  T3+T4               18                 21
                    vv
clus                 N0 N1 N2
  22Q LOSS MUTATED    7  7  1
  22Q LOSS WILD-TYPE 19  5  3
D62V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                7                 19
  N1                7                  5
  N2                1                  3
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   16  3 10
  22Q LOSS WILD-TYPE 41  3 47
D62V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               16                 41
  M1                3                  3
  MX               10                 47
D62V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   14 17
  22Q LOSS WILD-TYPE 26 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     14   17
  22Q LOSS WILD-TYPE   26   72
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               14                 26
  MALE                 17                 72
D62V8, continuous
D62V9, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  3 
        TCGA-GL-A59T         TCGA-IA-A40U         TCGA-PJ-A5Z9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D62V10, continuous

Clustering(63) Variable = XQ LOSS MUTATION ANALYSIS
D63V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   13  5
  XQ LOSS WILD-TYPE 91 10
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18               101 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5                10 
$`XQ LOSS MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-5155 
        0.03         0.69         9.63         7.33        10.09        15.12 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
        6.81         0.16        19.23         8.84        22.92        21.63 
TCGA-DW-5561 TCGA-DZ-6131 TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 
       13.61        79.82        11.05        14.63        14.07         3.68 

$`XQ LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
        1.61         4.60         0.03         0.07         0.69         0.72 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        0.03         0.10         0.03        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 
       30.31        25.08        44.61        19.56        16.37        11.41 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       10.98         4.83        50.50        28.14        26.40        20.58 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-BQ-5875 
        0.46         1.08         6.44         1.18         2.10        86.73 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        43.17        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        28.80        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        34.19        19.00        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       51.75        48.62        39.25        34.82        25.15       194.76 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-IA-A40U TCGA-IA-A40X 
        7.73         1.05         5.85         2.99         4.57        14.14 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        2.04         1.08         4.04         3.68         5.69 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.03              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            79.82            194.76 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            10.57             14.63 
[1] "0.0 - 79.8 (10.6)"  "0.0 - 194.8 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-8515        TCGA-A4-8516        TCGA-A4-8517        TCGA-A4-8518 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925        TCGA-B3-3926 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121        TCGA-B9-4113 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-B9-7268 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A5W8        TCGA-B9-A5W9        TCGA-BQ-5875 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
  "XQ LOSS MUTATED"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GL-8500        TCGA-GL-A4EM        TCGA-GL-A59R        TCGA-GL-A59T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-IZ-8195 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IZ-8196        TCGA-PJ-A5Z8        TCGA-PJ-A5Z9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "5.3"
D63V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         6        2         7        3
  XQ LOSS WILD-TYPE      63        8        23        7
D63V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 6                63
  STAGE II                2                 8
  STAGE III               7                23
  STAGE IV                3                 7
                   vv
clus                T1 T2 T3+T4
  XQ LOSS MUTATED    6  2    11
  XQ LOSS WILD-TYPE 68 14    28
D63V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1                  6                68
  T2                  2                14
  T3+T4              11                28
                   vv
clus                N0 N1 N2
  XQ LOSS MUTATED    2  5  1
  XQ LOSS WILD-TYPE 24  7  3
D63V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0               2                24
  N1               5                 7
  N2               1                 3
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED    7  2  8
  XQ LOSS WILD-TYPE 50  4 49
D63V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               7                50
  M1               2                 4
  MX               8                49
D63V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    8 11
  XQ LOSS WILD-TYPE 32 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      8   11
  XQ LOSS WILD-TYPE   32   78
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               8                32
  MALE                11                78
D63V8, continuous
D63V9, continuous
D63V10, continuous
> q(save="no")
