
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/READ-TP/4430019/transformed.cor.cli.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/READ-TP/4401907/READ-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=READ-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=READ-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/READ-TP/4401907/READ-TP.clin.merged.picked.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/4430019/transformed.cor.cli.txt"

nPatients in clinical file=336, in cluster file=162, common to both=162
[1] "Reduce the number of clustering variables from 80 to 77."
[1]  77 162
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               151 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               151 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               130 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               130 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               33               129 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               33               129 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               35               127 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               35               127 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               26               136 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               26               136 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               33               129 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               33               129 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               154 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               154 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               158 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4               158 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               31               131 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               31               131 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               21               141 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               21               141 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               39               123 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               39               123 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               35               127 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               35               127 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              101                61 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              101                61 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               90                72 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               90                72 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               41               121 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               41               121 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               88                74 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               88                74 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               41               121 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               41               121 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               32               130 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               32               130 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                150 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                150 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                156 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                156 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                28                134 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                28                134 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                24                138 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                24                138 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                129 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                129 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                140 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                140 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               108                 54 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               108                 54 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                154 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                154 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                157 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                157 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                124 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                38                124 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                38                124 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                38                124 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                154 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                154 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                29                133 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                29                133 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                153 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                153 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                156 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                156 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                29                133 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                29                133 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                30                132 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                30                132 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               103                 59 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               103                 59 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               142                 20 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               142                 20 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                152 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                152 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                153 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                153 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               128 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               34               128 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               42               120 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               42               120 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               24               138 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               24               138 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               151 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               151 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               156 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               156 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               147 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               147 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               152 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               152 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               57               105 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               57               105 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65                97 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65                97 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               137 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               25               137 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               39               123 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               39               123 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               14               148 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               14               148 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22               140 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22               140 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               74                88 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               74                88 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               151 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               151 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               22               140 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               22               140 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               21               141 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               21               141 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                32                130 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                32                130 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                125 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                125 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                138 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                138 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                29                133 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                29                133 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                139 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                23                139 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                21                141 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                21                141 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                154 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                154 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                64                 98 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                64                 98 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                70                 92 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                70                 92 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                153 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                153 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                15                147 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                15                147 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               104                 58 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               104                 58 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                137 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                137 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               124                 38 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               124                 38 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               135                 27 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               135                 27 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                139 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                23                139 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                20                142 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                20                142 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                138 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                24                138 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                64                 98 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                64                 98 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                56                106 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                56                106 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               25               137 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               25               137 
[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] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 162 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
         734          546          524          323          412          581 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
         387          761          316          441          257          467 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
         355          316           NA          365           NA           NA 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
          31           31           61           NA           31           31 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
          NA           NA           NA           NA           NA           30 
TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
          NA           NA           NA           30           NA           NA 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
          NA           NA           NA          242           29           NA 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
          31           NA           30           30           NA           NA 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
          31           NA           28           NA           31           30 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
          30           31           NA           NA           NA           NA 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 
          31           31           NA           31           31           NA 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
          NA           30          637          423          183          789 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
         700          518          484          396           31           31 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
         365          365         2130         1946          334           NA 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1519           NA           NA         1884         1246         1156 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
          15           44           21           22          140           55 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
         310          183          183           NA          211          285 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
         143          425         1825          243          334          335 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
         457          395          365          426          457         1095 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
         212          914          394          396          306          161 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        3845         1257         1741         3932          734         1566 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
         991           15           73          625          607          636 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
         517          556          482          538          497          496 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
         498          262          350          328          414          531 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
         364          257           NA          103           26           66 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
          12           31           20           21           16           33 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          23           14           NA         1696           NA          804 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=93,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 162 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=47, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  9  29 109  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  29 109  14 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  29 109  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  29 109  14 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
83 45 32 
[1] "table(vv)"
vv
N0 N1 N2 
83 45 32 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
83 45 32 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
83 45 32 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=21, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     6   2
  1P GAIN WILD-TYPE 111  11
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8               122 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                11 
$`1P GAIN MUTATED`
TCGA-AF-2692 TCGA-AG-3587 TCGA-AG-A026 TCGA-DC-6156 TCGA-DY-A1DF TCGA-EI-6884 
       13.55         1.02         1.94        15.02        24.13        10.78 
TCGA-EI-7004 TCGA-G5-6641 
        8.45        26.43 

$`1P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        10.62        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       10.39        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
       70.03        63.98        10.98        51.98        49.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         6.97        30.05        12.95        13.02        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        5.29       126.41        41.33        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.58         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.37         8.61        11.51        13.61        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        3.39         0.85         2.17         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.08         0.76         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.02              0.39 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            26.43            129.27 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           12.165            10.995 
[1] "1.0 - 26.4 (12.2)"  "0.4 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
[1] "hr=" "6.6"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1P GAIN MUTATED         1        1         3         0         0         0
  1P GAIN WILD-TYPE      29        7        35         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1P GAIN MUTATED            2          0          2        0         2
  1P GAIN WILD-TYPE          7         23         12       17         7
D1V3, multiclass
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     1   1   5   4
  1P GAIN WILD-TYPE   8  28 104  10
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1                 8
  T2               1                28
  T3               5               104
  T4               4                10
                   vv
clus                N0 N1 N2
  1P GAIN MUTATED    5  2  4
  1P GAIN WILD-TYPE 78 43 28
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               5                78
  N1               2                43
  N2               4                28
                   vv
clus                 M0  M1 M1A  MX
  1P GAIN MUTATED     9   0   1   1
  1P GAIN WILD-TYPE 114  22   1  12
D1V6, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0                9               114
  M1                0                22
  M1A               1                 1
  MX                1                12
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    5  6
  1P GAIN WILD-TYPE 69 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5    6
  1P GAIN WILD-TYPE   69   82
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               5                69
  MALE                 6                82
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     7   3
  1P GAIN WILD-TYPE 136  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7    3
  1P GAIN WILD-TYPE  136   10
                                clus
vv                               1P GAIN MUTATED 1P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        7               136
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  11
  1P GAIN WILD-TYPE   6 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   11
  1P GAIN WILD-TYPE    6  145
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 6
  YES              11               145
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED     9   1   0   0
  1P GAIN WILD-TYPE 112   1  12   3
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               9               112
  R1               1                 1
  R2               0                12
  RX               0                 3
D1V11, continuous

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   22  3
  1Q GAIN WILD-TYPE 95 10
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25               105 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                10 
$`1Q GAIN MUTATED`
TCGA-AF-2692 TCGA-AF-6672 TCGA-AG-3587 TCGA-AG-3999 TCGA-AG-A015 TCGA-AG-A01N 
       13.55        10.39         1.02         1.02        13.02        12.00 
TCGA-AG-A01W TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       70.03        51.98         1.94        38.01         0.49         0.69 
TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF 
        0.72         9.37        14.01        15.02       129.27        24.13 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7004 TCGA-F5-6813 TCGA-F5-6863 
        8.61        10.78        13.61         8.45         0.69         0.76 
TCGA-G5-6641 
       26.43 

$`1Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        10.62        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 
       12.00         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.94        23.01        17.03        15.91         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
        1.02        12.00        63.98        10.98        49.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       61.94        40.96         1.45         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.02         6.94         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         6.97        30.05        12.95        13.02        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.41        41.33        57.24        51.48        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.37 
TCGA-EI-6883 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.51        17.46        11.97         3.39         0.85         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        0.39         1.02         0.66         0.53         1.08         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.25        55.76        47.08 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.49              0.39 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.27            126.41 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            10.78             11.01 
[1] "0.5 - 129.3 (10.8)" "0.4 - 126.4 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1Q GAIN MUTATED         3        2         8         0         0         0
  1Q GAIN WILD-TYPE      27        6        30         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1Q GAIN MUTATED            3          2          6        4         2
  1Q GAIN WILD-TYPE          6         21          8       13         7
D2V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    3  3 18  8
  1Q GAIN WILD-TYPE  6 26 91  6
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               3                 6
  T2               3                26
  T3              18                91
  T4               8                 6
                   vv
clus                N0 N1 N2
  1Q GAIN MUTATED   14  7 10
  1Q GAIN WILD-TYPE 69 38 22
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              14                69
  N1               7                38
  N2              10                22
                   vv
clus                M0 M1 M1A MX
  1Q GAIN MUTATED   24  4   1  3
  1Q GAIN WILD-TYPE 99 18   1 10
D2V6, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               24                99
  M1                4                18
  M1A               1                 1
  MX                3                10
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   17 15
  1Q GAIN WILD-TYPE 57 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17   15
  1Q GAIN WILD-TYPE   57   73
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              17                57
  MALE                15                73
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    26   4
  1Q GAIN WILD-TYPE 117   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     26    4
  1Q GAIN WILD-TYPE  117    9
                                clus
vv                               1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       26               117
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1  31
  1Q GAIN WILD-TYPE   5 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   31
  1Q GAIN WILD-TYPE    5  125
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                1                 5
  YES              31               125
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   22  1  2  0
  1Q GAIN WILD-TYPE 99  1 10  3
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              22                99
  R1               1                 1
  R2               2                10
  RX               0                 3
D2V11, continuous

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   24  4
  2P GAIN WILD-TYPE 93  9
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               28               102 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                 9 
$`2P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-5654 TCGA-AG-3587 TCGA-AG-4007 
       24.13        17.95        17.23         8.45         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6897 TCGA-CL-5917 
        0.99        12.00        70.03        38.01         4.60        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        7.99        10.98        12.99        12.00        15.02        36.00 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6465 
      129.27        51.48        20.55        16.31        13.61         3.39 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.46        18.25        55.76        47.08 

$`2P GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       10.62        13.55        19.10        12.72        25.02        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 
       14.50        15.35        11.67        10.39        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        1.02         2.01         1.02         0.99         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.94        40.96         0.49         1.45         0.69         0.72 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 
        4.70        13.97        11.01        15.02        14.01         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.02        10.06         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.33        57.24        24.13        32.58         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.37         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6641 
        0.66         0.69         0.53         1.08         0.76        26.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.46              0.39 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           129.27            126.41 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           15.665            10.290 
[1] "0.5 - 129.3 (15.7)" "0.4 - 126.4 (10.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2P GAIN MUTATED         5        3         5         0         1         1
  2P GAIN WILD-TYPE      25        5        33         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2P GAIN MUTATED            0          4          6        4         3
  2P GAIN WILD-TYPE          9         19          8       13         6
D3V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    0  6 22  4
  2P GAIN WILD-TYPE  9 23 87 10
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               0                 9
  T2               6                23
  T3              22                87
  T4               4                10
                   vv
clus                N0 N1 N2
  2P GAIN MUTATED   14  7 11
  2P GAIN WILD-TYPE 69 38 21
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              14                69
  N1               7                38
  N2              11                21
                   vv
clus                 M0  M1 M1A  MX
  2P GAIN MUTATED    21   6   1   4
  2P GAIN WILD-TYPE 102  16   1   9
D3V6, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               21               102
  M1                6                16
  M1A               1                 1
  MX                4                 9
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   21 12
  2P GAIN WILD-TYPE 53 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     21   12
  2P GAIN WILD-TYPE   53   76
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              21                53
  MALE                12                76
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    33   0
  2P GAIN WILD-TYPE 110  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     33    0
  2P GAIN WILD-TYPE  110   13
                                clus
vv                               2P GAIN MUTATED 2P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       33               110
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1  32
  2P GAIN WILD-TYPE   5 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1   32
  2P GAIN WILD-TYPE    5  124
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                1                 5
  YES              32               124
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED   24  1  2  2
  2P GAIN WILD-TYPE 97  1 10  1
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              24                97
  R1               1                 1
  R2               2                10
  RX               2                 1
D3V11, continuous

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   25  4
  2Q GAIN WILD-TYPE 92  9
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               29               101 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4                 9 
$`2Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       24.13        17.95        17.23        10.39         8.45        15.35 
TCGA-AG-3587 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01N TCGA-AG-A01W 
        1.02         1.02         1.02         0.99        12.00        70.03 
TCGA-AG-A032 TCGA-AH-6897 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 
       38.01         4.60        60.00         7.99        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 
       15.02        36.00       129.27         2.40        16.31        13.61 
TCGA-F5-6465 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        3.39         0.76         0.46        18.25        47.08 

$`2Q GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       10.62        13.55        19.10        12.72        25.02        14.50 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
        0.99         1.02         1.02         1.02        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02         1.02        12.00        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.94         1.94        38.93        61.94        40.96         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         0.72         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 
        6.02         6.94         9.37         4.70        13.97        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       11.01        15.02        14.01         6.97        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.02        10.06         5.29       126.41        41.33        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.58         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.37         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45         0.85         2.17         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6641 
        0.69         0.53         1.08        55.76        26.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.39 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           129.27            126.41 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            12.99             10.78 
[1] "0.5 - 129.3 (13.0)" "0.4 - 126.4 (10.8)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2Q GAIN MUTATED         5        3         6         0         1         1
  2Q GAIN WILD-TYPE      25        5        32         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2Q GAIN MUTATED            0          4          7        4         2
  2Q GAIN WILD-TYPE          9         19          7       13         7
D4V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    0  6 23  5
  2Q GAIN WILD-TYPE  9 23 86  9
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               0                 9
  T2               6                23
  T3              23                86
  T4               5                 9
                   vv
clus                N0 N1 N2
  2Q GAIN MUTATED   15  7 12
  2Q GAIN WILD-TYPE 68 38 20
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              15                68
  N1               7                38
  N2              12                20
                   vv
clus                 M0  M1 M1A  MX
  2Q GAIN MUTATED    23   6   1   4
  2Q GAIN WILD-TYPE 100  16   1   9
D4V6, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               23               100
  M1                6                16
  M1A               1                 1
  MX                4                 9
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   22 13
  2Q GAIN WILD-TYPE 52 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     22   13
  2Q GAIN WILD-TYPE   52   75
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              22                52
  MALE                13                75
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    35   0
  2Q GAIN WILD-TYPE 108  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     35    0
  2Q GAIN WILD-TYPE  108   13
                                clus
vv                               2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       35               108
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  33
  2Q GAIN WILD-TYPE   4 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   33
  2Q GAIN WILD-TYPE    4  123
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                2                 4
  YES              33               123
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED   27  0  2  2
  2Q GAIN WILD-TYPE 94  2 10  1
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              27                94
  R1               0                 2
  R2               2                10
  RX               2                 1
D4V11, continuous

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   19  1
  3P GAIN WILD-TYPE 98 12
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               20               110 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                12 
$`3P GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A016 
       25.02        11.67        10.39         1.02         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A020 TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 
       12.00        10.98         9.37        10.98        12.99        15.02 
TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-7002 
       12.95        41.33       129.27         2.40        18.28        11.97 
TCGA-F5-6702 TCGA-F5-6811 
        2.17         1.02 

$`3P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3575 
       12.72        10.39        14.50         8.45        15.35        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         0.99        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J 
       25.94        23.01        17.03        15.91        13.02         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        63.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.93        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.02         6.94         4.70        13.97        60.00         7.99 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02        12.00        14.01        36.00         6.97 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       30.05        13.02        10.06         5.29       126.41        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.58         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.37         8.61        11.51        10.78        13.61        17.46 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
        8.45         3.39         0.85         0.39         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.08         0.76         0.46        18.25        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.02              0.39 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           129.27            126.41 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           11.325            10.895 
[1] "1.0 - 129.3 (11.3)" "0.4 - 126.4 (10.9)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3P GAIN MUTATED         2        0         8         0         0         2
  3P GAIN WILD-TYPE      28        8        30         2         2         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3P GAIN MUTATED            1          4          1        4         4
  3P GAIN WILD-TYPE          8         19         13       13         5
D5V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    1  3 20  2
  3P GAIN WILD-TYPE  8 26 89 12
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1                 8
  T2               3                26
  T3              20                89
  T4               2                12
                   vv
clus                N0 N1 N2
  3P GAIN MUTATED   11  7  8
  3P GAIN WILD-TYPE 72 38 24
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              11                72
  N1               7                38
  N2               8                24
                   vv
clus                 M0  M1 M1A  MX
  3P GAIN MUTATED    17   4   2   3
  3P GAIN WILD-TYPE 106  18   0  10
D5V6, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               17               106
  M1                4                18
  M1A               2                 0
  MX                3                10
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   13 13
  3P GAIN WILD-TYPE 61 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     13   13
  3P GAIN WILD-TYPE   61   75
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              13                61
  MALE                13                75
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    25   1
  3P GAIN WILD-TYPE 118  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     25    1
  3P GAIN WILD-TYPE  118   12
                                clus
vv                               3P GAIN MUTATED 3P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       25               118
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  24
  3P GAIN WILD-TYPE   4 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   24
  3P GAIN WILD-TYPE    4  132
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                2                 4
  YES              24               132
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    19   0   1   0
  3P GAIN WILD-TYPE 102   2  11   3
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              19               102
  R1               0                 2
  R2               1                11
  RX               0                 3
D5V11, continuous

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   24  2
  3Q GAIN WILD-TYPE 93 11
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               26               104 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                11 
$`3Q GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3726 TCGA-AG-3896 
       25.02        10.39        11.67        10.39         7.96         1.02 
TCGA-AG-4001 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A020 TCGA-CI-6623 TCGA-CL-5917 
        1.02         1.02        12.00        10.98         9.37        60.00 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC 
       10.98        12.99        15.02        12.95        13.02        41.33 
TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6810 
        2.40        18.28        16.31        11.97         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6863 
        1.02         0.76 

$`3Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3575 TCGA-AG-3581 
       12.72        14.50         8.45        15.35        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       17.03        15.91        13.02         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       63.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       40.96        38.01         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
        4.70        13.97         7.99        11.01        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 
       14.01        36.00         6.97        30.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.41        57.24       129.27        24.13        51.48        32.58 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
        0.49        20.55        19.96        20.91        17.00        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.37         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 
       13.61        17.46         8.45         3.39         0.85         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.08         0.46        18.25        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.39              0.46 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            60.00            129.27 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            10.98             11.26 
[1] "0.4 - 60.0 (11.0)"  "0.5 - 129.3 (11.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3Q GAIN MUTATED         3        0        10         0         0         2
  3Q GAIN WILD-TYPE      27        8        28         2         2         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3Q GAIN MUTATED            1          6          2        4         4
  3Q GAIN WILD-TYPE          8         17         12       13         5
D6V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    1  4 25  3
  3Q GAIN WILD-TYPE  8 25 84 11
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               1                 8
  T2               4                25
  T3              25                84
  T4               3                11
                   vv
clus                N0 N1 N2
  3Q GAIN MUTATED   14 10  9
  3Q GAIN WILD-TYPE 69 35 23
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              14                69
  N1              10                35
  N2               9                23
                   vv
clus                 M0  M1 M1A  MX
  3Q GAIN MUTATED    22   5   2   4
  3Q GAIN WILD-TYPE 101  17   0   9
D6V6, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               22               101
  M1                5                17
  M1A               2                 0
  MX                4                 9
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   17 16
  3Q GAIN WILD-TYPE 57 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     17   16
  3Q GAIN WILD-TYPE   57   72
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              17                57
  MALE                16                72
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    32   1
  3Q GAIN WILD-TYPE 111  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     32    1
  3Q GAIN WILD-TYPE  111   12
                                clus
vv                               3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       32               111
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  31
  3Q GAIN WILD-TYPE   4 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   31
  3Q GAIN WILD-TYPE    4  125
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                2                 4
  YES              31               125
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED   26  0  1  1
  3Q GAIN WILD-TYPE 95  2 11  2
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              26                95
  R1               0                 2
  R2               1                11
  RX               1                 2
D6V11, continuous

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     4   1
  4P GAIN WILD-TYPE 113  12
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5               125 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                12 
$`4P GAIN MUTATED`
TCGA-AG-4022 TCGA-AG-A011 TCGA-DC-4749 TCGA-DY-A1DG TCGA-EI-6510 
        0.99        17.03        11.01        51.48        18.28 

$`4P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        63.98        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.93        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.94         9.37         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        10.98        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         6.97        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.58         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.37         8.61        11.51        10.78        13.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.25        55.76        47.08        26.43 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.99              0.39 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            51.48            129.27 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            17.03             10.98 
[1] "1.0 - 51.5 (17.0)"  "0.4 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4P GAIN MUTATED         2        1         2         0         0         1
  4P GAIN WILD-TYPE      28        7        36         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4P GAIN MUTATED            0          0          0        0         2
  4P GAIN WILD-TYPE          9         23         14       17         7
D7V3, multiclass
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     0   3   5   0
  4P GAIN WILD-TYPE   9  26 104  14
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                 9
  T2               3                26
  T3               5               104
  T4               0                14
                   vv
clus                N0 N1 N2
  4P GAIN MUTATED    6  2  0
  4P GAIN WILD-TYPE 77 43 32
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               6                77
  N1               2                43
  N2               0                32
                   vv
clus                 M0  M1 M1A  MX
  4P GAIN MUTATED     5   1   0   2
  4P GAIN WILD-TYPE 118  21   2  11
D7V6, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0                5               118
  M1                1                21
  M1A               0                 2
  MX                2                11
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  6
  4P GAIN WILD-TYPE 72 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    6
  4P GAIN WILD-TYPE   72   82
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                72
  MALE                 6                82
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     8   0
  4P GAIN WILD-TYPE 135  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8    0
  4P GAIN WILD-TYPE  135   13
                                clus
vv                               4P GAIN MUTATED 4P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        8               135
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   8
  4P GAIN WILD-TYPE   6 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    8
  4P GAIN WILD-TYPE    6  148
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 6
  YES               8               148
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     6   0   0   0
  4P GAIN WILD-TYPE 115   2  12   3
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               6               115
  R1               0                 2
  R2               0                12
  RX               0                 3
D7V11, continuous

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     1   1
  4Q GAIN WILD-TYPE 116  12
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               128 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                12 
$`4Q GAIN MUTATED`
TCGA-AG-3893 TCGA-DY-A1DG 
        0.99        51.48 

$`4Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.02         6.02         6.94         9.37         4.70        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.00         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        14.01        15.02        36.00         6.97        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.02        10.06         5.29       126.41        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        32.58         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.37         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       10.78        13.61        17.46        11.97         8.45         3.39 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        0.85         2.17         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.08         0.76         0.46        18.25        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.99              0.39 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            51.48            129.27 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           26.235            10.995 
[1] "1.0 - 51.5 (26.2)"  "0.4 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               128 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3894        TCGA-AG-3896 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4Q GAIN MUTATED         1        0         1         0         0         0
  4Q GAIN WILD-TYPE      29        8        37         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4Q GAIN MUTATED            0          1          0        0         1
  4Q GAIN WILD-TYPE          9         22         14       17         8
D8V3, multiclass
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     0   1   3   0
  4Q GAIN WILD-TYPE   9  28 106  14
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                 9
  T2               1                28
  T3               3               106
  T4               0                14
                   vv
clus                N0 N1 N2
  4Q GAIN MUTATED    2  2  0
  4Q GAIN WILD-TYPE 81 43 32
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               2                81
  N1               2                43
  N2               0                32
                   vv
clus                 M0  M1 M1A  MX
  4Q GAIN MUTATED     3   1   0   0
  4Q GAIN WILD-TYPE 120  21   2  13
D8V6, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0                3               120
  M1                1                21
  M1A               0                 2
  MX                0                13
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  4
  4Q GAIN WILD-TYPE 74 84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    4
  4Q GAIN WILD-TYPE   74   84
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               0                74
  MALE                 4                84
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4   0
  4Q GAIN WILD-TYPE 139  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    0
  4Q GAIN WILD-TYPE  139   13
                                clus
vv                               4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        4               139
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   4
  4Q GAIN WILD-TYPE   6 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    4
  4Q GAIN WILD-TYPE    6  152
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 6
  YES               4               152
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     3   0   0   0
  4Q GAIN WILD-TYPE 118   2  12   3
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               3               118
  R1               0                 2
  R2               0                12
  RX               0                 3
D8V11, continuous

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   25  2
  5P GAIN WILD-TYPE 92 11
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               27               103 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                11 
$`5P GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3883 
       25.02        11.67        10.39         1.02         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G 
        1.02         1.02        13.02        12.00        12.00        38.93 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6156 
       40.96        38.01         0.69         0.72        12.99        15.02 
TCGA-DC-6158 TCGA-DC-6683 TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6702 
        6.97        10.06         2.40        16.31        11.51         2.17 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
        1.02         0.53         0.76 

$`5P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3575 
       12.72        10.39        14.50         8.45        15.35        12.00 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        1.02         2.01         1.02         0.99         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 
        0.95         1.02         0.99         0.99         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4008 TCGA-AG-4022 
        0.99         0.99         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.91         1.02         1.02        70.03        63.98        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 
       51.98        49.94         1.94        61.94         0.49         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.70        13.97        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 
       11.01        15.02        12.00        14.01        36.00        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.02         5.29       126.41        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.58         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.37         8.61        10.78        13.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       11.97         8.45         3.39         0.85         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.08         0.46        18.25        55.76        47.08 
TCGA-G5-6641 
       26.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.53              0.39 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            40.96            129.27 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            10.06             11.97 
[1] "0.5 - 41.0 (10.1)"  "0.4 - 129.3 (12.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5P GAIN MUTATED         6        0         5         0         1         0
  5P GAIN WILD-TYPE      24        8        33         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5P GAIN MUTATED            1          6          4        5         2
  5P GAIN WILD-TYPE          8         17         10       12         7
D9V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    1  9 16  5
  5P GAIN WILD-TYPE  8 20 93  9
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                 8
  T2               9                20
  T3              16                93
  T4               5                 9
                   vv
clus                N0 N1 N2
  5P GAIN MUTATED   13 10  7
  5P GAIN WILD-TYPE 70 35 25
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              13                70
  N1              10                35
  N2               7                25
                   vv
clus                 M0  M1 M1A  MX
  5P GAIN MUTATED    22   5   1   3
  5P GAIN WILD-TYPE 101  17   1  10
D9V6, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               22               101
  M1                5                17
  M1A               1                 1
  MX                3                10
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   10 21
  5P GAIN WILD-TYPE 64 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10   21
  5P GAIN WILD-TYPE   64   67
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              10                64
  MALE                21                67
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    31   0
  5P GAIN WILD-TYPE 112  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     31    0
  5P GAIN WILD-TYPE  112   13
                                clus
vv                               5P GAIN MUTATED 5P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       31               112
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     2  29
  5P GAIN WILD-TYPE   4 127
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2   29
  5P GAIN WILD-TYPE    4  127
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                2                 4
  YES              29               127
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   23  0  4  0
  5P GAIN WILD-TYPE 98  2  8  3
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              23                98
  R1               0                 2
  R2               4                 8
  RX               0                 3
D9V11, continuous

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    17   0
  5Q GAIN WILD-TYPE 100  13
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17               113 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                13 
$`5Q GAIN MUTATED`
TCGA-AF-6655 TCGA-AG-3582 TCGA-AG-3883 TCGA-AG-4007 TCGA-AG-A01L TCGA-AG-A01N 
       11.67         1.02         1.02         1.02        12.00        12.00 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6683 
       40.96        38.01         0.69         0.72        12.99        10.06 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6814 
       16.31        11.51        11.97         1.02         0.53 

$`5Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       10.39        12.00         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        0.99         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02         1.02        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 
       49.94         1.94        38.93        61.94         0.49         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.70        13.97        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.00        14.01        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
        6.97        30.05        12.95        13.02         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.33        57.24       129.27        24.13        51.48        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.37         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       10.78        13.61        17.46         8.45         3.39         0.85 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
        2.17         0.39         0.66         0.69         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.25        55.76        47.08        26.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.53              0.39 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            40.96            129.27 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            11.51             10.98 
[1] "0.5 - 41.0 (11.5)"  "0.4 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "hr="     "7.8e+07"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5Q GAIN MUTATED         3        0         3         0         1         0
  5Q GAIN WILD-TYPE      27        8        35         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5Q GAIN MUTATED            1          5          3        4         0
  5Q GAIN WILD-TYPE          8         18         11       13         9
D10V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED    0  6 13  2
  5Q GAIN WILD-TYPE  9 23 96 12
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                 9
  T2               6                23
  T3              13                96
  T4               2                12
                   vv
clus                N0 N1 N2
  5Q GAIN MUTATED    8  7  5
  5Q GAIN WILD-TYPE 75 38 27
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               8                75
  N1               7                38
  N2               5                27
                   vv
clus                 M0  M1 M1A  MX
  5Q GAIN MUTATED    16   4   0   1
  5Q GAIN WILD-TYPE 107  18   2  12
D10V6, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               16               107
  M1                4                18
  M1A               0                 2
  MX                1                12
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    7 14
  5Q GAIN WILD-TYPE 67 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   14
  5Q GAIN WILD-TYPE   67   74
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               7                67
  MALE                14                74
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    21   0
  5Q GAIN WILD-TYPE 122  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     21    0
  5Q GAIN WILD-TYPE  122   13
                                clus
vv                               5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       21               122
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  21
  5Q GAIN WILD-TYPE   6 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   21
  5Q GAIN WILD-TYPE    6  135
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 6
  YES              21               135
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    16   0   3   0
  5Q GAIN WILD-TYPE 105   2   9   3
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              16               105
  R1               0                 2
  R2               3                 9
  RX               0                 3
D10V11, continuous

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   30  2
  6P GAIN WILD-TYPE 87 11
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               32                98 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                11 
$`6P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       24.13        10.62        25.02        10.39        14.50        15.35 
TCGA-AG-3587 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 
       13.02         1.02        12.00         0.72        10.19         6.02 
TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DE 
        9.37        12.99        12.00        15.02        36.00       129.27 
TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       20.55        15.85        17.69         3.39         2.17         0.39 
TCGA-G5-6233 TCGA-G5-6641 
       18.25        26.43 

$`6P GAIN WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       17.95        17.23        13.55        19.10        12.72         8.45 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         0.99         0.92         1.02         0.99         0.99 
TCGA-AG-3999 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       23.01        17.03        15.91         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        4.60         1.81         6.02         6.94         4.70        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 
       60.00         7.99        10.98        11.01        15.02        14.01 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.97        30.05        12.95        13.02        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.41        41.33        57.24        24.13        51.48        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.37         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6811 
       13.61        17.46        11.97         8.45         0.85         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.08         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.39              0.46 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           129.27            126.41 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           11.310            10.995 
[1] "0.4 - 129.3 (11.3)" "0.5 - 126.4 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6P GAIN MUTATED         7        1         6         0         1         1
  6P GAIN WILD-TYPE      23        7        32         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6P GAIN MUTATED            1          8          3        5         4
  6P GAIN WILD-TYPE          8         15         11       12         5
D11V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    4  5 25  5
  6P GAIN WILD-TYPE  5 24 84  9
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4                 5
  T2               5                24
  T3              25                84
  T4               5                 9
                   vv
clus                N0 N1 N2
  6P GAIN MUTATED   15 12 11
  6P GAIN WILD-TYPE 68 33 21
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              15                68
  N1              12                33
  N2              11                21
                   vv
clus                M0 M1 M1A MX
  6P GAIN MUTATED   24  8   1  5
  6P GAIN WILD-TYPE 99 14   1  8
D11V6, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               24                99
  M1                8                14
  M1A               1                 1
  MX                5                 8
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   17 22
  6P GAIN WILD-TYPE 57 66
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     17   22
  6P GAIN WILD-TYPE   57   66
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              17                57
  MALE                22                66
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    37   1
  6P GAIN WILD-TYPE 106  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     37    1
  6P GAIN WILD-TYPE  106   12
                                clus
vv                               6P GAIN MUTATED 6P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       37               106
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     4  35
  6P GAIN WILD-TYPE   2 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   35
  6P GAIN WILD-TYPE    2  121
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                4                 2
  YES              35               121
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED   28  0  5  0
  6P GAIN WILD-TYPE 93  2  7  3
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              28                93
  R1               0                 2
  R2               5                 7
  RX               0                 3
D11V11, continuous

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   27  2
  6Q GAIN WILD-TYPE 90 11
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               29               101 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                11 
$`6Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       24.13        10.62        25.02        10.39        14.50        15.35 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 
        1.02         1.02         1.02         1.02         0.99        13.02 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
        1.02        12.00         0.72        10.19         6.02         9.37 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6506 
       12.99        12.00        15.02        36.00        51.48        20.55 
TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       15.85        17.69         3.39         2.17         0.39 

$`6Q GAIN WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       17.95        17.23        13.55        19.10        12.72         8.45 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        1.02         0.99         0.99         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        0.99         1.02         1.02        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L 
       25.94        23.01        17.03        15.91         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        63.98        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.93        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         4.60         1.81         6.02         6.94         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01        15.02 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       14.01         6.97        30.05        12.95        13.02        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.41        41.33        57.24       129.27        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.58         0.49         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        16.34        16.31        16.37         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       10.78        13.61        17.46        11.97         8.45         0.85 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.25        55.76        47.08        26.43 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.39              0.46 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            51.48            129.27 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            10.62             11.01 
[1] "0.4 - 51.5 (10.6)"  "0.5 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6Q GAIN MUTATED         6        1         5         0         0         1
  6Q GAIN WILD-TYPE      24        7        33         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6Q GAIN MUTATED            0          8          2        5         5
  6Q GAIN WILD-TYPE          9         15         12       12         4
D12V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    3  4 23  5
  6Q GAIN WILD-TYPE  6 25 86  9
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3                 6
  T2               4                25
  T3              23                86
  T4               5                 9
                   vv
clus                N0 N1 N2
  6Q GAIN MUTATED   13 12  9
  6Q GAIN WILD-TYPE 70 33 23
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              13                70
  N1              12                33
  N2               9                23
                   vv
clus                 M0  M1 M1A  MX
  6Q GAIN MUTATED    20   9   1   4
  6Q GAIN WILD-TYPE 103  13   1   9
D12V6, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               20               103
  M1                9                13
  M1A               1                 1
  MX                4                 9
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   15 20
  6Q GAIN WILD-TYPE 59 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15   20
  6Q GAIN WILD-TYPE   59   68
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              15                59
  MALE                20                68
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    34   0
  6Q GAIN WILD-TYPE 109  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     34    0
  6Q GAIN WILD-TYPE  109   13
                                clus
vv                               6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       34               109
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     4  31
  6Q GAIN WILD-TYPE   2 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4   31
  6Q GAIN WILD-TYPE    2  125
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                4                 2
  YES              31               125
                   vv
clus                R0 R1 R2 RX
  6Q GAIN MUTATED   24  0  5  0
  6Q GAIN WILD-TYPE 97  2  7  3
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              24                97
  R1               0                 2
  R2               5                 7
  RX               0                 3
D12V11, continuous

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   74 10
  7P GAIN WILD-TYPE 43  3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               84                46 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                 3 
$`7P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        12.72        25.02        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 
       14.50         8.45        15.35        11.67         1.02         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3893 
        1.02         0.99         0.99         0.99         0.99         0.99 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H 
        1.02         1.02         1.02         1.02         0.99        25.94 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       70.03         1.94        38.93        38.01         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 
        0.72         4.60        10.19         6.02         9.37         4.70 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       60.00         7.99        10.98        11.01        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        36.00         6.97        13.02        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
      126.41        41.33        57.24       129.27        24.13         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.40        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.31        11.51        10.78        13.61        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        0.85         2.17         0.39         1.02         0.66         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

$`7P GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3583 
       10.62        13.55        19.10        10.39        12.00         2.01 
TCGA-AG-3586 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3887 
        1.02         7.96         0.95         1.02         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         0.99         1.02        20.94        13.91         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       23.01        17.03        63.98        10.98        51.98        49.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
       61.94        40.96         1.45         1.81         6.02         6.94 
TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DG 
       13.97        15.02        14.01        30.05        12.95        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 
       32.58        20.55        19.96        17.00        16.37         8.61 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
       17.46         3.39         0.53         1.08 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.39              0.53 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           129.27             63.98 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           10.880            12.475 
[1] "0.4 - 129.3 (10.9)" "0.5 - 64.0 (12.5)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
[1] "hr=" "2"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7P GAIN MUTATED        17        4        21         1         2         1
  7P GAIN WILD-TYPE      13        4        17         1         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7P GAIN MUTATED            3         20         11       11         6
  7P GAIN WILD-TYPE          6          3          3        6         3
D13V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    4 18 67 11
  7P GAIN WILD-TYPE  5 11 42  3
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               4                 5
  T2              18                11
  T3              67                42
  T4              11                 3
                   vv
clus                N0 N1 N2
  7P GAIN MUTATED   46 31 22
  7P GAIN WILD-TYPE 37 14 10
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              46                37
  N1              31                14
  N2              22                10
                   vv
clus                M0 M1 M1A MX
  7P GAIN MUTATED   74 15   1  9
  7P GAIN WILD-TYPE 49  7   1  4
D13V6, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               74                49
  M1               15                 7
  M1A               1                 1
  MX                9                 4
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   43 58
  7P GAIN WILD-TYPE 31 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     43   58
  7P GAIN WILD-TYPE   31   30
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              43                31
  MALE                58                30
D13V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   95  4
  7P GAIN WILD-TYPE 48  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     95    4
  7P GAIN WILD-TYPE   48    9
                                clus
vv                               7P GAIN MUTATED 7P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       95                48
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
D13V9, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5 96
  7P GAIN WILD-TYPE  1 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5   96
  7P GAIN WILD-TYPE    1   60
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                5                 1
  YES              96                60
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   74  2  8  3
  7P GAIN WILD-TYPE 47  0  4  0
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              74                47
  R1               2                 0
  R2               8                 4
  RX               3                 0
D13V11, continuous

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   66  8
  7Q GAIN WILD-TYPE 51  5
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               74                56 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                8                 5 
$`7Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       24.13        17.95        12.72        25.02        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 
        8.45        15.35        11.67         1.02         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3893 TCGA-AG-3896 
        0.99         0.99         0.99         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A014 
        1.02         1.02         1.02         0.99        25.94        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       13.02         1.02         1.02        12.00        12.00        70.03 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.93        38.01         0.49         0.69         0.72         4.60 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       10.19         6.02         9.37        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       11.01        12.99        12.00        15.02        36.00         6.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.02        10.06         5.29        41.33        57.24        24.13 
TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        0.49        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.31        11.51        11.97         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        1.02         0.69         0.76         0.46        18.25        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`7Q GAIN WILD-TYPE`
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-6672 TCGA-AG-3575 
       17.23        10.62        13.55        19.10        10.39        12.00 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3883 
        2.01         1.02         7.96         0.95         1.02         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
        0.92         1.02         0.99         1.02        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        6.02        23.01        17.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 
       49.94         1.94        61.94        40.96         1.45         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6155 
        6.02         6.94         4.70        13.97        15.02        14.01 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
       30.05        12.95       126.41       129.27        51.48        32.58 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 
        2.40        20.55        19.96        17.00        16.37         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6812 
       10.78        13.61        17.46         8.45         3.39         0.66 
TCGA-F5-6814 TCGA-F5-6861 
        0.53         1.08 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.39              0.53 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            70.03            129.27 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           10.995            11.490 
[1] "0.4 - 70.0 (11.0)"  "0.5 - 129.3 (11.5)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
[1] "hr=" "1.7"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7Q GAIN MUTATED        16        3        15         1         2         1
  7Q GAIN WILD-TYPE      14        5        23         1         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7Q GAIN MUTATED            2         20         11       10         5
  7Q GAIN WILD-TYPE          7          3          3        7         4
D14V3, multiclass
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    4 17 59  9
  7Q GAIN WILD-TYPE  5 12 50  5
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               4                 5
  T2              17                12
  T3              59                50
  T4               9                 5
                   vv
clus                N0 N1 N2
  7Q GAIN MUTATED   38 29 21
  7Q GAIN WILD-TYPE 45 16 11
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              38                45
  N1              29                16
  N2              21                11
                   vv
clus                M0 M1 M1A MX
  7Q GAIN MUTATED   64 14   1  9
  7Q GAIN WILD-TYPE 59  8   1  4
D14V6, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               64                59
  M1               14                 8
  M1A               1                 1
  MX                9                 4
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   37 53
  7Q GAIN WILD-TYPE 37 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     37   53
  7Q GAIN WILD-TYPE   37   35
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              37                37
  MALE                53                35
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   85  3
  7Q GAIN WILD-TYPE 58 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     85    3
  7Q GAIN WILD-TYPE   58   10
                                clus
vv                               7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       85                58
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
D14V9, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5 85
  7Q GAIN WILD-TYPE  1 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5   85
  7Q GAIN WILD-TYPE    1   71
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                5                 1
  YES              85                71
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   67  1  8  3
  7Q GAIN WILD-TYPE 54  1  4  0
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              67                54
  R1               1                 1
  R2               8                 4
  RX               3                 0
D14V11, continuous

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   29  4
  8P GAIN WILD-TYPE 88  9
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33                97 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                 9 
$`8P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-3896 
       24.13        12.72        11.67         1.02         0.92         1.02 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        1.02         0.99         1.02        12.00        70.03        63.98 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 
       38.01         0.49         0.69         0.72         6.02         9.37 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD 
        7.99        12.99        15.02        13.02        41.33        57.24 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6465 
       24.13         0.49        17.00        16.31        11.51         3.39 
TCGA-F5-6810 TCGA-F5-6863 TCGA-G5-6572 
        0.39         0.76        47.08 

$`8P GAIN WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        10.62        13.55        19.10        25.02 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 
       10.39        14.50         8.45        15.35        10.39        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99         7.96         0.95         0.99         0.99         1.02 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A023 
       15.91        13.02         1.02        12.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       49.94         1.94        38.93        61.94        40.96         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        4.60         1.81        10.19         6.02         6.94         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       13.97        60.00        10.98        11.01        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       14.01        36.00         6.97        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
        5.29       126.41       129.27        51.48        32.58         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.37         8.61        10.78        13.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         0.85         2.17         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.08         0.46        18.25        55.76 
TCGA-G5-6641 
       26.43 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.39              0.46 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            70.03            129.27 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            11.51             10.98 
[1] "0.4 - 70.0 (11.5)"  "0.5 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8P GAIN MUTATED         2        4        13         1         1         1
  8P GAIN WILD-TYPE      28        4        25         1         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8P GAIN MUTATED            1          4          4        6         1
  8P GAIN WILD-TYPE          8         19         10       11         8
D15V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    1  3 32  4
  8P GAIN WILD-TYPE  8 26 77 10
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1                 8
  T2               3                26
  T3              32                77
  T4               4                10
                   vv
clus                N0 N1 N2
  8P GAIN MUTATED   22  9  8
  8P GAIN WILD-TYPE 61 36 24
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              22                61
  N1               9                36
  N2               8                24
                   vv
clus                M0 M1 M1A MX
  8P GAIN MUTATED   29  7   1  3
  8P GAIN WILD-TYPE 94 15   1 10
D15V6, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               29                94
  M1                7                15
  M1A               1                 1
  MX                3                10
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   17 24
  8P GAIN WILD-TYPE 57 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     17   24
  8P GAIN WILD-TYPE   57   64
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              17                57
  MALE                24                64
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    37   3
  8P GAIN WILD-TYPE 106  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     37    3
  8P GAIN WILD-TYPE  106   10
                                clus
vv                               8P GAIN MUTATED 8P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       37               106
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     2  39
  8P GAIN WILD-TYPE   4 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2   39
  8P GAIN WILD-TYPE    4  117
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                2                 4
  YES              39               117
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED   25  0  5  1
  8P GAIN WILD-TYPE 96  2  7  2
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              25                96
  R1               0                 2
  R2               5                 7
  RX               1                 2
D15V11, continuous

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   59 11
  8Q GAIN WILD-TYPE 58  2
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               70                60 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11                 2 
$`8Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        17.95        17.23        10.62        13.55        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3586 
       25.02        10.39        11.67        10.39         1.02         1.02 
TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3999 
        1.02         7.96         1.02         0.92         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
        1.02         1.02         0.99        25.94        17.03        15.91 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        1.02         1.02        12.00        70.03        63.98        51.98 
TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.01         0.49         1.45         0.69         0.72 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       10.19         6.02         9.37         4.70        60.00         7.99 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       12.99        14.01        15.02         6.97        13.02        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.41        41.33        57.24        24.13        32.58         0.49 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.00        16.34        16.31        11.51        10.78        13.61 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
        3.39         2.17         0.39         1.02         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        55.76        47.08        26.43 

$`8Q GAIN WILD-TYPE`
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3575 TCGA-AG-3581 
       19.10        14.50         8.45        15.35        12.00         1.02 
TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
        2.01         0.99         0.99         0.95         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-A002 
        1.02         1.02         0.99         0.99         1.02        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 
       13.91         6.02        23.01        13.02        12.00        10.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 
       49.94        38.93        61.94        40.96         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        6.02         6.94        13.97        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE 
       12.00        36.00        30.05        12.95         5.29       129.27 
TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 
       15.85        17.69        16.37         8.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        8.45         0.85         0.66         0.69         0.53         1.08 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.39              0.53 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           126.41            129.27 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            10.70             11.49 
[1] "0.4 - 126.4 (10.7)" "0.5 - 129.3 (11.5)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G5-6572        TCGA-G5-6641 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
[1] "hr=" "3.4"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8Q GAIN MUTATED         9        5        23         1         2         2
  8Q GAIN WILD-TYPE      21        3        15         1         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8Q GAIN MUTATED            5         10         11       13         2
  8Q GAIN WILD-TYPE          4         13          3        4         7
D16V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    3 11 64  9
  8Q GAIN WILD-TYPE  6 18 45  5
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               3                 6
  T2              11                18
  T3              64                45
  T4               9                 5
                   vv
clus                N0 N1 N2
  8Q GAIN MUTATED   41 23 22
  8Q GAIN WILD-TYPE 42 22 10
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              41                42
  N1              23                22
  N2              22                10
                   vv
clus                M0 M1 M1A MX
  8Q GAIN MUTATED   61 15   1  9
  8Q GAIN WILD-TYPE 62  7   1  4
D16V6, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               61                62
  M1               15                 7
  M1A               1                 1
  MX                9                 4
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   40 48
  8Q GAIN WILD-TYPE 34 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     40   48
  8Q GAIN WILD-TYPE   34   40
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              40                34
  MALE                48                40
D16V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   81  4
  8Q GAIN WILD-TYPE 62  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     81    4
  8Q GAIN WILD-TYPE   62    9
                                clus
vv                               8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       81                62
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
D16V9, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5 83
  8Q GAIN WILD-TYPE  1 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5   83
  8Q GAIN WILD-TYPE    1   73
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                5                 1
  YES              83                73
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   58  2  9  2
  8Q GAIN WILD-TYPE 63  0  3  1
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              58                63
  R1               2                 0
  R2               9                 3
  RX               2                 1
D16V11, continuous

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED   27  4
  9P GAIN WILD-TYPE 90  9
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               31                99 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                4                 9 
$`9P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3587 
       17.95        17.23        12.72        10.39        11.67         1.02 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A01W 
        0.99         7.96         0.99         1.02         1.02        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-4745 
       10.98        51.98        38.01         0.69         0.72        10.98 
TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 
       36.00       129.27         2.40        11.51        10.78         8.45 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        2.17         0.39         0.69         1.08         0.46        18.25 
TCGA-G5-6641 
       26.43 

$`9P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       24.13        10.62        13.55        19.10        25.02        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
        8.45        15.35        10.39        12.00         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        2.01         1.02         0.99         0.95         1.02         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         0.99        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.94        23.01        17.03        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 
        1.02        12.00        12.00        63.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 
       38.93        61.94        40.96         0.49         1.45         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.70        13.97        60.00         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       12.99        12.00        14.01        15.02         6.97        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.02        10.06         5.29       126.41        41.33 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.58         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.31        16.37         8.61        13.61        17.46 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       11.97         3.39         0.85         1.02         0.66         0.53 
TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.76        55.76        47.08 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.39              0.49 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           129.27            126.41 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            10.39             12.00 
[1] "0.4 - 129.3 (10.4)" "0.5 - 126.4 (12.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
[1] "hr=" "1.3"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9P GAIN MUTATED         6        1        11         0         2         2
  9P GAIN WILD-TYPE      24        7        27         2         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9P GAIN MUTATED            4          3          5        3         2
  9P GAIN WILD-TYPE          5         20          9       14         7
D17V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    1  7 29  4
  9P GAIN WILD-TYPE  8 22 80 10
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               1                 8
  T2               7                22
  T3              29                80
  T4               4                10
                   vv
clus                N0 N1 N2
  9P GAIN MUTATED   20 10 10
  9P GAIN WILD-TYPE 63 35 22
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              20                63
  N1              10                35
  N2              10                22
                   vv
clus                M0 M1 M1A MX
  9P GAIN MUTATED   34  5   0  2
  9P GAIN WILD-TYPE 89 17   2 11
D17V6, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               34                89
  M1                5                17
  M1A               0                 2
  MX                2                11
D17V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   18 23
  9P GAIN WILD-TYPE 56 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     18   23
  9P GAIN WILD-TYPE   56   65
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              18                56
  MALE                23                65
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    35   5
  9P GAIN WILD-TYPE 108   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     35    5
  9P GAIN WILD-TYPE  108    8
                                clus
vv                               9P GAIN MUTATED 9P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       35               108
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  40
  9P GAIN WILD-TYPE   5 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   40
  9P GAIN WILD-TYPE    5  116
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 5
  YES              40               116
                   vv
clus                R0 R1 R2 RX
  9P GAIN MUTATED   36  0  2  0
  9P GAIN WILD-TYPE 85  2 10  3
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              36                85
  R1               0                 2
  R2               2                10
  RX               0                 3
D17V11, continuous

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   20  3
  9Q GAIN WILD-TYPE 97 10
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               23               107 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                10 
$`9Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3605 TCGA-AG-3878 
       17.95        12.72        10.39        11.67         0.99         0.99 
TCGA-AG-3896 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-4745 
        1.02        10.98        51.98        38.01         0.72        10.98 
TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6810 
       36.00       129.27         2.40        11.51        10.78         0.39 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.69         1.08         0.46        18.25        26.43 

$`9Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       24.13        17.23        10.62        13.55        19.10        25.02 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 
       14.50         8.45        15.35        10.39        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        1.02         2.01         1.02         1.02         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.95         1.02         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        63.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.94        40.96         0.49         1.45         0.69         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.70        13.97        60.00         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       12.99        12.00        14.01        15.02         6.97        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.02        10.06         5.29       126.41        41.33 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.58         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.31        16.37         8.61        13.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       11.97         8.45         3.39         0.85         2.17         1.02 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.66         0.53         0.76        55.76        47.08 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.39              0.49 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           129.27            126.41 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            10.98             11.97 
[1] "0.4 - 129.3 (11.0)" "0.5 - 126.4 (12.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9Q GAIN MUTATED         4        0        10         0         2         2
  9Q GAIN WILD-TYPE      26        8        28         2         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9Q GAIN MUTATED            4          2          3        3         0
  9Q GAIN WILD-TYPE          5         21         11       14         9
D18V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    1  5 23  3
  9Q GAIN WILD-TYPE  8 24 86 11
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               1                 8
  T2               5                24
  T3              23                86
  T4               3                11
                   vv
clus                N0 N1 N2
  9Q GAIN MUTATED   16  8  7
  9Q GAIN WILD-TYPE 67 37 25
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              16                67
  N1               8                37
  N2               7                25
                   vv
clus                M0 M1 M1A MX
  9Q GAIN MUTATED   26  4   0  2
  9Q GAIN WILD-TYPE 97 18   2 11
D18V6, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               26                97
  M1                4                18
  M1A               0                 2
  MX                2                11
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   12 20
  9Q GAIN WILD-TYPE 62 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     12   20
  9Q GAIN WILD-TYPE   62   68
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              12                62
  MALE                20                68
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    27   4
  9Q GAIN WILD-TYPE 116   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     27    4
  9Q GAIN WILD-TYPE  116    9
                                clus
vv                               9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       27               116
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  31
  9Q GAIN WILD-TYPE   5 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   31
  9Q GAIN WILD-TYPE    5  125
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 5
  YES              31               125
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED   27  0  2  0
  9Q GAIN WILD-TYPE 94  2 10  3
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              27                94
  R1               0                 2
  R2               2                10
  RX               0                 3
D18V11, continuous

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     8   1
  10P GAIN WILD-TYPE 109  12
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                121 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 12 
$`10P GAIN MUTATED`
TCGA-AF-2689 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-4745 
       17.95        15.91         1.02        70.03        10.19        10.98 
TCGA-DY-A1DF TCGA-F5-6571 TCGA-F5-6812 
       24.13         0.85         0.66 

$`10P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       10.39        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
       17.03        13.02         1.02        12.00        12.00        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       40.96        38.01         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.70        13.97        60.00         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        14.01        15.02        36.00         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.02        10.06         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.33        57.24       129.27        51.48        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.37         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.61        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
        3.39         2.17         0.39         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76         0.46        18.25        55.76        47.08 
TCGA-G5-6641 
       26.43 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.66               0.39 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             70.03             129.27 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             10.98              11.01 
[1] "0.7 - 70.0 (11.0)"  "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10P GAIN MUTATED         1        1         4         0         0         0
  10P GAIN WILD-TYPE      29        7        34         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10P GAIN MUTATED            0          3          1        2         0
  10P GAIN WILD-TYPE          9         20         13       15         9
D19V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    0  1 11  0
  10P GAIN WILD-TYPE  9 28 98 14
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3               11                 98
  T4                0                 14
                    vv
clus                 N0 N1 N2
  10P GAIN MUTATED    6  3  3
  10P GAIN WILD-TYPE 77 42 29
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                6                 77
  N1                3                 42
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  10P GAIN MUTATED     9   2   0   0
  10P GAIN WILD-TYPE 114  20   2  13
D19V6, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                 9                114
  M1                 2                 20
  M1A                0                  2
  MX                 0                 13
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6  6
  10P GAIN WILD-TYPE 68 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    6
  10P GAIN WILD-TYPE   68   82
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                6                 68
  MALE                  6                 82
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12   0
  10P GAIN WILD-TYPE 131  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE  131   13
                                clus
vv                               10P GAIN MUTATED 10P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        12                131
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  11
  10P GAIN WILD-TYPE   5 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   11
  10P GAIN WILD-TYPE    5  145
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 1                  5
  YES               11                145
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    10   0   1   0
  10P GAIN WILD-TYPE 111   2  11   3
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               10                111
  R1                0                  2
  R2                1                 11
  RX                0                  3
D19V11, continuous

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     5   1
  10Q GAIN WILD-TYPE 112  12
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                124 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 12 
$`10Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AG-3999 TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-4745 TCGA-DY-A1DF 
       17.95         1.02        70.03        10.19        10.98        24.13 

$`10Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       10.39        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        0.99         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.70        13.97        60.00         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        14.01        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.97        30.05        12.95        13.02        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
      126.41        41.33        57.24       129.27        51.48        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.37 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         3.39         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.08         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        55.76        47.08        26.43 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.02               0.39 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             70.03             129.27 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            14.465             10.995 
[1] "1.0 - 70.0 (14.5)"  "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10Q GAIN MUTATED         0        1         0         0         0         0
  10Q GAIN WILD-TYPE      30        7        38         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10Q GAIN MUTATED            0          2          2        1         0
  10Q GAIN WILD-TYPE          9         21         12       16         9
D20V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     0   0   6   0
  10Q GAIN WILD-TYPE   9  29 103  14
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  9
  T2                0                 29
  T3                6                103
  T4                0                 14
                    vv
clus                 N0 N1 N2
  10Q GAIN MUTATED    1  2  3
  10Q GAIN WILD-TYPE 82 43 29
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                1                 82
  N1                2                 43
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  10Q GAIN MUTATED     4   1   0   0
  10Q GAIN WILD-TYPE 119  21   2  13
D20V6, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                 4                119
  M1                 1                 21
  M1A                0                  2
  MX                 0                 13
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    5  1
  10Q GAIN WILD-TYPE 69 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    1
  10Q GAIN WILD-TYPE   69   87
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                 69
  MALE                  1                 87
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     6   0
  10Q GAIN WILD-TYPE 137  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    0
  10Q GAIN WILD-TYPE  137   13
                                clus
vv                               10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                137
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   5
  10Q GAIN WILD-TYPE   5 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    5
  10Q GAIN WILD-TYPE    5  151
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                  5
  YES                5                151
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     5   0   0   0
  10Q GAIN WILD-TYPE 116   2  12   3
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                5                116
  R1                0                  2
  R2                0                 12
  RX                0                  3
D20V11, continuous

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED   21  3
  11P GAIN WILD-TYPE 96 10
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                24                106 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 10 
$`11P GAIN MUTATED`
TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-4001 
       17.23        10.39        11.67        12.00         1.02         1.02 
TCGA-AG-4007 TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 
        1.02        12.00         4.60        10.19         9.37         4.70 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       11.01        12.99        12.00        36.00        30.05       126.41 
TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-G5-6233 
        2.40        16.31        13.61         0.39         1.02        18.25 

$`11P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3581 
       25.02        14.50         8.45        15.35        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        1.02         2.01         1.02         0.99         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4008 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        63.98        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.93        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72         1.81         6.02         6.02         6.94 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 
       13.97        60.00         7.99        10.98        15.02        14.01 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02         6.97        12.95        13.02        10.06         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.33        57.24       129.27        24.13        51.48        32.58 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.37         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46        11.97         8.45         3.39         0.85 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        2.17         0.66         0.69         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.46 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            126.41             129.27 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             11.34              10.98 
[1] "0.4 - 126.4 (11.3)" "0.5 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "11P GAIN MUTATED"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "11P GAIN MUTATED"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "11P GAIN MUTATED"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11P GAIN MUTATED         7        1         8         0         1         0
  11P GAIN WILD-TYPE      23        7        30         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11P GAIN MUTATED            1          3          2        3         1
  11P GAIN WILD-TYPE          8         20         12       14         8
D21V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    1  8 17  2
  11P GAIN WILD-TYPE  8 21 92 12
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                1                  8
  T2                8                 21
  T3               17                 92
  T4                2                 12
                    vv
clus                 N0 N1 N2
  11P GAIN MUTATED   17  6  5
  11P GAIN WILD-TYPE 66 39 27
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               17                 66
  N1                6                 39
  N2                5                 27
                    vv
clus                  M0  M1 M1A  MX
  11P GAIN MUTATED    22   5   0   0
  11P GAIN WILD-TYPE 101  17   2  13
D21V6, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                22                101
  M1                 5                 17
  M1A                0                  2
  MX                 0                 13
D21V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   12 16
  11P GAIN WILD-TYPE 62 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     12   16
  11P GAIN WILD-TYPE   62   72
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               12                 62
  MALE                 16                 72
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    28   0
  11P GAIN WILD-TYPE 115  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     28    0
  11P GAIN WILD-TYPE  115   13
                                clus
vv                               11P GAIN MUTATED 11P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        28                115
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  27
  11P GAIN WILD-TYPE   5 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   27
  11P GAIN WILD-TYPE    5  129
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                  5
  YES               27                129
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED   22  0  2  0
  11P GAIN WILD-TYPE 99  2 10  3
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               22                 99
  R1                0                  2
  R2                2                 10
  RX                0                  3
D21V11, continuous

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED   20  2
  11Q GAIN WILD-TYPE 97 11
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                22                108 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 11 
$`11Q GAIN MUTATED`
TCGA-AF-2690 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3883 TCGA-AG-4001 
       17.23        10.39        12.00         1.02         1.02         1.02 
TCGA-AG-4007 TCGA-AG-A01N TCGA-AH-6897 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 
        1.02        12.00         4.60         9.37         4.70        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A0XA TCGA-EI-6514 
       12.99        12.00        15.02        36.00       126.41        16.31 
TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       13.61         0.39         1.02         0.66 

$`11Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       25.02        14.50         8.45        15.35        11.67        10.39 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 
        1.02         1.02         2.01         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        7.96         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4008 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        63.98        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.93        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        6.94        13.97        60.00         7.99        10.98        15.02 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       14.01         6.97        30.05        12.95        13.02        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29        41.33        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.58         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.37 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        11.51        10.78        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        3.39         0.85         2.17         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.46 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            126.41             129.27 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            10.700             11.245 
[1] "0.4 - 126.4 (10.7)" "0.5 - 129.3 (11.2)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "11Q GAIN MUTATED"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11Q GAIN MUTATED         7        1         7         0         0         0
  11Q GAIN WILD-TYPE      23        7        31         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11Q GAIN MUTATED            0          2          1        3         2
  11Q GAIN WILD-TYPE          9         21         13       14         7
D22V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    1  7 13  3
  11Q GAIN WILD-TYPE  8 22 96 11
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                1                  8
  T2                7                 22
  T3               13                 96
  T4                3                 11
                    vv
clus                 N0 N1 N2
  11Q GAIN MUTATED   16  4  4
  11Q GAIN WILD-TYPE 67 41 28
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               16                 67
  N1                4                 41
  N2                4                 28
                    vv
clus                  M0  M1 M1A  MX
  11Q GAIN MUTATED    18   5   1   0
  11Q GAIN WILD-TYPE 105  17   1  13
D22V6, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                18                105
  M1                 5                 17
  M1A                1                  1
  MX                 0                 13
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   11 13
  11Q GAIN WILD-TYPE 63 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     11   13
  11Q GAIN WILD-TYPE   63   75
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               11                 63
  MALE                 13                 75
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    24   0
  11Q GAIN WILD-TYPE 119  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     24    0
  11Q GAIN WILD-TYPE  119   13
                                clus
vv                               11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        24                119
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  24
  11Q GAIN WILD-TYPE   6 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   24
  11Q GAIN WILD-TYPE    6  132
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  6
  YES               24                132
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    18   0   2   0
  11Q GAIN WILD-TYPE 103   2  10   3
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               18                103
  R1                0                  2
  R2                2                 10
  RX                0                  3
D22V11, continuous

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   23  3
  12P GAIN WILD-TYPE 94 10
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                26                104 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 10 
$`12P GAIN MUTATED`
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3587 TCGA-AG-3726 
       12.72        25.02         8.45        10.39         1.02         7.96 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A014 TCGA-AG-A015 
        1.02         0.92         1.02         1.02        15.91        13.02 
TCGA-AG-A02G TCGA-AG-A02N TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       38.93        61.94        60.00        13.02        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
      126.41        32.58        19.96        18.28        17.69        13.61 
TCGA-EI-7002 TCGA-G5-6233 
       11.97        18.25 

$`12P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 
       10.39        14.50        15.35        11.67        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         0.99         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02         0.99         0.99         1.02         0.99         0.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        25.94        23.01        17.03         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.94         1.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        6.02         6.94         9.37         4.70        13.97         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC 
       15.02        36.00         6.97        30.05        12.95        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       20.55        20.91        17.00        15.85        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 
       16.37         8.61        11.51        10.78        17.46         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        3.39         0.85         2.17         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.08         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.92               0.39 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            126.41             129.27 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             13.02              10.70 
[1] "0.9 - 126.4 (13.0)" "0.4 - 129.3 (10.7)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12P GAIN MUTATED         7        3         9         0         1         0
  12P GAIN WILD-TYPE      23        5        29         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12P GAIN MUTATED            1          3          4        4         1
  12P GAIN WILD-TYPE          8         20         10       13         8
D23V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    1  9 21  2
  12P GAIN WILD-TYPE  8 20 88 12
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                1                  8
  T2                9                 20
  T3               21                 88
  T4                2                 12
                    vv
clus                 N0 N1 N2
  12P GAIN MUTATED   20  6  7
  12P GAIN WILD-TYPE 63 39 25
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               20                 63
  N1                6                 39
  N2                7                 25
                    vv
clus                 M0 M1 M1A MX
  12P GAIN MUTATED   26  3   0  4
  12P GAIN WILD-TYPE 97 19   2  9
D23V6, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                26                 97
  M1                 3                 19
  M1A                0                  2
  MX                 4                  9
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   14 19
  12P GAIN WILD-TYPE 60 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     14   19
  12P GAIN WILD-TYPE   60   69
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               14                 60
  MALE                 19                 69
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    28   4
  12P GAIN WILD-TYPE 115   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     28    4
  12P GAIN WILD-TYPE  115    9
                                clus
vv                               12P GAIN MUTATED 12P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        28                115
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3  30
  12P GAIN WILD-TYPE   3 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   30
  12P GAIN WILD-TYPE    3  126
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 3                  3
  YES               30                126
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED   24  0  2  2
  12P GAIN WILD-TYPE 97  2 10  1
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               24                 97
  R1                0                  2
  R2                2                 10
  RX                2                  1
D23V11, continuous

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    14   3
  12Q GAIN WILD-TYPE 103  10
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                17                113 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 10 
$`12Q GAIN MUTATED`
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-A015 TCGA-AG-A02G 
       12.72         8.45         1.02         1.02        13.02        38.93 
TCGA-AG-A02N TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 
       61.94        13.02        10.06       126.41        32.58        19.96 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-G5-6233 
       18.28        17.69        13.61        11.97        18.25 

$`12Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       25.02        10.39        14.50        15.35        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       12.00         1.02         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        0.99         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.94        23.01        17.03        15.91         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        12.00        70.03        63.98        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.94         1.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.02         6.02         6.94         9.37         4.70        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.00         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        14.01        15.02        36.00         6.97        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.95         5.29        41.33        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        16.34        16.31        16.37         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       10.78        17.46         8.45         3.39         0.85         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.02               0.39 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            126.41             129.27 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             13.61              10.39 
[1] "1.0 - 126.4 (13.6)" "0.4 - 129.3 (10.4)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12Q GAIN MUTATED         4        2         6         0         1         0
  12Q GAIN WILD-TYPE      26        6        32         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12Q GAIN MUTATED            1          3          1        3         1
  12Q GAIN WILD-TYPE          8         20         13       14         8
D24V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    1  6 14  1
  12Q GAIN WILD-TYPE  8 23 95 13
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                1                  8
  T2                6                 23
  T3               14                 95
  T4                1                 13
                    vv
clus                 N0 N1 N2
  12Q GAIN MUTATED   13  6  3
  12Q GAIN WILD-TYPE 70 39 29
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               13                 70
  N1                6                 39
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  12Q GAIN MUTATED    18   3   0   1
  12Q GAIN WILD-TYPE 105  19   2  12
D24V6, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                18                105
  M1                 3                 19
  M1A                0                  2
  MX                 1                 12
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   11 11
  12Q GAIN WILD-TYPE 63 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     11   11
  12Q GAIN WILD-TYPE   63   77
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               11                 63
  MALE                 11                 77
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    19   2
  12Q GAIN WILD-TYPE 124  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     19    2
  12Q GAIN WILD-TYPE  124   11
                                clus
vv                               12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        19                124
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  21
  12Q GAIN WILD-TYPE   5 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   21
  12Q GAIN WILD-TYPE    5  135
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  5
  YES               21                135
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    17   0   2   0
  12Q GAIN WILD-TYPE 104   2  10   3
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               17                104
  R1                0                  2
  R2                2                 10
  RX                0                  3
D24V11, continuous

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   78 13
  13Q GAIN WILD-TYPE 39  0
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                91                 39 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                  0 
$`13Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        10.62        13.55        19.10        25.02 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 
       10.39        14.50        15.35        11.67        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3605 TCGA-AG-3727 
        1.02         2.01         1.02         1.02         0.99         0.95 
TCGA-AG-3742 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.99         0.92         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02         1.02         0.99         6.02        25.94 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.91        13.02         1.02        12.00        70.03        63.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.94         1.94        38.93        38.01         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        0.69         0.72         4.60         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.70        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        12.00        36.00         6.97        30.05 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06        41.33        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       32.58         0.49        20.55        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.37        11.51        10.78 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         3.39         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.66         0.69         0.76        18.25        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`13Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3599 TCGA-AG-3726 
       24.13        12.72         8.45        12.00         0.99         7.96 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A008 
        1.02         0.99         1.02         1.02        20.94        13.91 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A02N 
       23.01        17.03         1.02        12.00        10.98        61.94 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 
       40.96         1.45         1.81        10.19         6.02        14.01 
TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-EF-5831 
       15.02        12.95        13.02         5.29       126.41         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       19.96        20.91         8.61        13.61        17.46         8.45 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        0.53         1.08         0.46 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.39               0.46 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            129.27             126.41 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             11.01              10.98 
[1] "0.4 - 129.3 (11.0)" "0.5 - 126.4 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-G5-6641 
  "13Q GAIN MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-G5-6641 
  "13Q GAIN MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-G5-6641 
  "13Q GAIN MUTATED" 
[1] "hr="     "2.8e+08"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  13Q GAIN MUTATED        19        4        20         2         2         4
  13Q GAIN WILD-TYPE      11        4        18         0         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  13Q GAIN MUTATED            6         19         11       12         5
  13Q GAIN WILD-TYPE          3          4          3        5         4
D25V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    7 17 71 12
  13Q GAIN WILD-TYPE  2 12 38  2
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                  2
  T2               17                 12
  T3               71                 38
  T4               12                  2
                    vv
clus                 N0 N1 N2
  13Q GAIN MUTATED   47 35 24
  13Q GAIN WILD-TYPE 36 10  8
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               47                 36
  N1               35                 10
  N2               24                  8
                    vv
clus                 M0 M1 M1A MX
  13Q GAIN MUTATED   79 16   0 12
  13Q GAIN WILD-TYPE 44  6   2  1
D25V6, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                79                 44
  M1                16                  6
  M1A                0                  2
  MX                12                  1
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   48 60
  13Q GAIN WILD-TYPE 26 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     48   60
  13Q GAIN WILD-TYPE   26   28
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               48                 26
  MALE                 60                 28
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   101   3
  13Q GAIN WILD-TYPE  42  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    101    3
  13Q GAIN WILD-TYPE   42   10
                                clus
vv                               13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       101                 42
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     3 105
  13Q GAIN WILD-TYPE   3  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3  105
  13Q GAIN WILD-TYPE    3   51
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 3                  3
  YES              105                 51
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED   76  2  8  2
  13Q GAIN WILD-TYPE 45  0  4  1
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               76                 45
  R1                2                  0
  R2                8                  4
  RX                2                  1
D25V11, continuous

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     7   0
  14Q GAIN WILD-TYPE 110  13
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                123 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                 13 
$`14Q GAIN MUTATED`
TCGA-AF-6136 TCGA-AG-3999 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01Y TCGA-EI-6512 
       15.35         1.02        15.91        12.00        63.98        17.69 
TCGA-EI-6885 
       13.61 

$`14Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       12.72        25.02        10.39        14.50         8.45        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       10.39        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        0.99         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
       13.02         1.02         1.02        12.00        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.94         1.94        38.93        61.94        40.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.01         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.70        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        14.01        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.97        30.05        12.95        13.02        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.41        41.33        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.58         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       17.00        18.28        15.85        16.34        16.31        16.37 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        11.51        10.78        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        3.39         0.85         2.17         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.08         0.76         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.02               0.39 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             63.98             129.27 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             15.35              10.78 
[1] "1.0 - 64.0 (15.3)"  "0.4 - 129.3 (10.8)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"14Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"14Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"14Q GAIN WILD-TYPE" 
[1] "hr="     "7.6e+07"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  14Q GAIN MUTATED         1        1         1         0         0         0
  14Q GAIN WILD-TYPE      29        7        37         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  14Q GAIN MUTATED            0          3          1        1         0
  14Q GAIN WILD-TYPE          9         20         13       16         9
D26V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     0   1   7   0
  14Q GAIN WILD-TYPE   9  28 102  14
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3                7                102
  T4                0                 14
                    vv
clus                 N0 N1 N2
  14Q GAIN MUTATED    3  4  1
  14Q GAIN WILD-TYPE 80 41 31
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                3                 80
  N1                4                 41
  N2                1                 31
                    vv
clus                  M0  M1 M1A  MX
  14Q GAIN MUTATED     6   1   0   1
  14Q GAIN WILD-TYPE 117  21   2  12
D26V6, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                 6                117
  M1                 1                 21
  M1A                0                  2
  MX                 1                 12
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    5  3
  14Q GAIN WILD-TYPE 69 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5    3
  14Q GAIN WILD-TYPE   69   85
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                5                 69
  MALE                  3                 85
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     8   0
  14Q GAIN WILD-TYPE 135  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      8    0
  14Q GAIN WILD-TYPE  135   13
                                clus
vv                               14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         8                135
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1   7
  14Q GAIN WILD-TYPE   5 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    7
  14Q GAIN WILD-TYPE    5  149
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 1                  5
  YES                7                149
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED     7   0   0   0
  14Q GAIN WILD-TYPE 114   2  12   3
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                7                114
  R1                0                  2
  R2                0                 12
  RX                0                  3
D26V11, continuous

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     4   0
  15Q GAIN WILD-TYPE 113  13
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                126 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                 13 
$`15Q GAIN MUTATED`
TCGA-AF-3400 TCGA-AG-4001 TCGA-AG-A01W TCGA-EI-7004 
       12.72         1.02        70.03         8.45 

$`15Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       10.39        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        0.99         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         6.97        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.58         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.37         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       13.61        17.46        11.97         3.39         0.85         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.02               0.39 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             70.03             129.27 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            10.585             10.995 
[1] "1.0 - 70.0 (10.6)"  "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"15Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"15Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"15Q GAIN WILD-TYPE" 
[1] "hr="     "7.6e+07"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  15Q GAIN MUTATED         0        1         2         0         0         0
  15Q GAIN WILD-TYPE      30        7        36         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  15Q GAIN MUTATED            0          0          1        0         1
  15Q GAIN WILD-TYPE          9         23         13       17         8
D27V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED     0   0   3   2
  15Q GAIN WILD-TYPE   9  29 106  12
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                  9
  T2                0                 29
  T3                3                106
  T4                2                 12
                    vv
clus                 N0 N1 N2
  15Q GAIN MUTATED    3  0  2
  15Q GAIN WILD-TYPE 80 45 30
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                3                 80
  N1                0                 45
  N2                2                 30
                    vv
clus                  M0  M1 M1A  MX
  15Q GAIN MUTATED     5   0   0   0
  15Q GAIN WILD-TYPE 118  22   2  13
D27V6, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                 5                118
  M1                 0                 22
  M1A                0                  2
  MX                 0                 13
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    4  1
  15Q GAIN WILD-TYPE 70 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    1
  15Q GAIN WILD-TYPE   70   87
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  1                 87
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3   2
  15Q GAIN WILD-TYPE 140  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE  140   11
                                clus
vv                               15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         3                140
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1   4
  15Q GAIN WILD-TYPE   5 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    4
  15Q GAIN WILD-TYPE    5  152
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 1                  5
  YES                4                152
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     5   0   0   0
  15Q GAIN WILD-TYPE 116   2  12   3
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                5                116
  R1                0                  2
  R2                0                 12
  RX                0                  3
D27V11, continuous

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   28  2
  16P GAIN WILD-TYPE 89 11
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                30                100 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 11 
$`16P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3726 TCGA-AG-3896 
       17.95        25.02        15.35        11.67         7.96         1.02 
TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
        1.02         0.99        15.91        13.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6622 TCGA-CI-6623 
       12.00        38.93        38.01         0.72         6.94         9.37 
TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF 
       60.00        11.01        12.99        12.00        10.06        24.13 
TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6863 
       17.69        16.31         3.39         2.17         0.39         0.76 

$`16P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 
       10.39        14.50         8.45        10.39        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.94        40.96         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
        4.60         1.81        10.19         6.02         6.02         4.70 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 
       13.97         7.99        10.98        15.02        14.01        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       36.00         6.97        30.05        12.95        13.02         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
      126.41        41.33        57.24       129.27        51.48        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        16.34        16.37         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       10.78        13.61        17.46        11.97         8.45         0.85 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        1.02         0.66         0.69         0.53         1.08         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        55.76        47.08        26.43 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.39               0.46 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             60.00             129.27 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            11.835             10.880 
[1] "0.4 - 60.0 (11.8)"  "0.5 - 129.3 (10.9)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16P GAIN MUTATED         7        1         6         1         0         1
  16P GAIN WILD-TYPE      23        7        32         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16P GAIN MUTATED            1         10          4        4         2
  16P GAIN WILD-TYPE          8         13         10       13         7
D28V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    2  8 24  4
  16P GAIN WILD-TYPE  7 21 85 10
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                2                  7
  T2                8                 21
  T3               24                 85
  T4                4                 10
                    vv
clus                 N0 N1 N2
  16P GAIN MUTATED   16 13  8
  16P GAIN WILD-TYPE 67 32 24
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               16                 67
  N1               13                 32
  N2                8                 24
                    vv
clus                 M0 M1 M1A MX
  16P GAIN MUTATED   28  6   0  4
  16P GAIN WILD-TYPE 95 16   2  9
D28V6, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                28                 95
  M1                 6                 16
  M1A                0                  2
  MX                 4                  9
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   19 19
  16P GAIN WILD-TYPE 55 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     19   19
  16P GAIN WILD-TYPE   55   69
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               19                 55
  MALE                 19                 69
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    38   0
  16P GAIN WILD-TYPE 105  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     38    0
  16P GAIN WILD-TYPE  105   13
                                clus
vv                               16P GAIN MUTATED 16P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        38                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     2  36
  16P GAIN WILD-TYPE   4 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   36
  16P GAIN WILD-TYPE    4  120
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 2                  4
  YES               36                120
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED   27  0  4  1
  16P GAIN WILD-TYPE 94  2  8  2
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               27                 94
  R1                0                  2
  R2                4                  8
  RX                1                  2
D28V11, continuous

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   28  4
  16Q GAIN WILD-TYPE 89  9
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                32                 98 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                  9 
$`16Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3896 
       17.95        25.02        10.39        15.35        11.67         1.02 
TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
        1.02         0.99        15.91        13.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 
       12.00        38.93        38.01         0.72         9.37        60.00 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF TCGA-DY-A1DG 
       11.01        12.99        12.00        10.06        24.13        51.48 
TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
       17.69        16.31         3.39         2.17         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6863 
        0.69         0.76 

$`16Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       14.50         8.45        10.39        12.00         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        2.01         1.02         1.02         0.99         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.94        40.96         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 
        4.70        13.97         7.99        10.98        15.02        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         6.97        30.05        12.95        13.02 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
        5.29       126.41        41.33        57.24       129.27        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        16.34        16.37         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       10.78        13.61        17.46        11.97         8.45         0.85 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        1.02         0.53         1.08         0.46        18.25        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.39               0.46 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             60.00             129.27 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            11.835             10.880 
[1] "0.4 - 60.0 (11.8)"  "0.5 - 129.3 (10.9)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16Q GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16Q GAIN MUTATED         6        1         7         0         0         1
  16Q GAIN WILD-TYPE      24        7        31         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16Q GAIN MUTATED            1          9          4        4         3
  16Q GAIN WILD-TYPE          8         14         10       13         6
D29V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    2  7 26  3
  16Q GAIN WILD-TYPE  7 22 83 11
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                2                  7
  T2                7                 22
  T3               26                 83
  T4                3                 11
                    vv
clus                 N0 N1 N2
  16Q GAIN MUTATED   15 14  8
  16Q GAIN WILD-TYPE 68 31 24
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               15                 68
  N1               14                 31
  N2                8                 24
                    vv
clus                 M0 M1 M1A MX
  16Q GAIN MUTATED   26  8   0  4
  16Q GAIN WILD-TYPE 97 14   2  9
D29V6, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                26                 97
  M1                 8                 14
  M1A                0                  2
  MX                 4                  9
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   18 20
  16Q GAIN WILD-TYPE 56 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     18   20
  16Q GAIN WILD-TYPE   56   68
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               18                 56
  MALE                 20                 68
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    38   0
  16Q GAIN WILD-TYPE 105  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     38    0
  16Q GAIN WILD-TYPE  105   13
                                clus
vv                               16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        38                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  36
  16Q GAIN WILD-TYPE   4 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   36
  16Q GAIN WILD-TYPE    4  120
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 2                  4
  YES               36                120
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED   28  0  3  1
  16Q GAIN WILD-TYPE 93  2  9  2
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               28                 93
  R1                0                  2
  R2                3                  9
  RX                1                  2
D29V11, continuous

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     5   0
  17P GAIN WILD-TYPE 112  13
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                125 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                 13 
$`17P GAIN MUTATED`
TCGA-AG-3587 TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 TCGA-G5-6641 
        1.02         9.37        12.00        13.02        26.43 

$`17P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.02         6.94         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.99        10.98        11.01        15.02        12.99        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        36.00         6.97        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.41        41.33        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.58         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.37         8.61        11.51        10.78        13.61 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46        11.97         8.45         3.39         0.85         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76         0.46        18.25        55.76        47.08 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.02               0.39 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             26.43             129.27 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             12.00              10.98 
[1] "1.0 - 26.4 (12.0)"  "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
  "17P GAIN MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
  "17P GAIN MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
  "17P GAIN MUTATED" 
[1] "hr="     "2.6e+07"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17P GAIN MUTATED         3        0         2         0         0         0
  17P GAIN WILD-TYPE      27        8        36         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17P GAIN MUTATED            1          0          1        0         1
  17P GAIN WILD-TYPE          8         23         13       17         8
D30V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED     2   2   3   1
  17P GAIN WILD-TYPE   7  27 106  13
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                2                  7
  T2                2                 27
  T3                3                106
  T4                1                 13
                    vv
clus                 N0 N1 N2
  17P GAIN MUTATED    5  1  2
  17P GAIN WILD-TYPE 78 44 30
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                5                 78
  N1                1                 44
  N2                2                 30
                    vv
clus                  M0  M1 M1A  MX
  17P GAIN MUTATED     6   1   0   1
  17P GAIN WILD-TYPE 117  21   2  12
D30V6, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                 6                117
  M1                 1                 21
  M1A                0                  2
  MX                 1                 12
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  4
  17P GAIN WILD-TYPE 70 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    4
  17P GAIN WILD-TYPE   70   84
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  4                 84
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     7   1
  17P GAIN WILD-TYPE 136  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    1
  17P GAIN WILD-TYPE  136   12
                                clus
vv                               17P GAIN MUTATED 17P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         7                136
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0   8
  17P GAIN WILD-TYPE   6 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    8
  17P GAIN WILD-TYPE    6  148
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  6
  YES                8                148
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     7   0   0   0
  17P GAIN WILD-TYPE 114   2  12   3
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                7                114
  R1                0                  2
  R2                0                 12
  RX                0                  3
D30V11, continuous

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   20  2
  17Q GAIN WILD-TYPE 97 11
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                108 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 11 
$`17Q GAIN MUTATED`
TCGA-AF-2690 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A014 
       17.23        12.00         1.02         1.02         1.02        15.91 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 
        1.02        12.00         0.69         4.60         6.02        12.00 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 
       13.02        10.06        51.48        17.00        18.28        16.31 
TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6864 TCGA-G5-6641 
       11.97         1.02         0.46        26.43 

$`17Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 
       10.39         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         0.99        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L 
       25.94        23.01        17.03        13.02         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        63.98        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.93        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72         1.81        10.19         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.70        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.99        14.01        15.02        36.00         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95         5.29       126.41        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        32.58         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       19.96        20.91        15.85        17.69        16.34        16.37 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.61        17.46         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
        3.39         0.85         2.17         0.39         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.08         0.76        18.25        55.76        47.08 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.46               0.39 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             51.48             129.27 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            11.985             10.980 
[1] "0.5 - 51.5 (12.0)"  "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
  "17Q GAIN MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
  "17Q GAIN MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
  "17Q GAIN MUTATED" 
[1] "hr=" "1.9"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17Q GAIN MUTATED         4        1         8         0         0         1
  17Q GAIN WILD-TYPE      26        7        30         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17Q GAIN MUTATED            1          2          5        4         3
  17Q GAIN WILD-TYPE          8         21          9       13         6
D31V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    1  6 20  2
  17Q GAIN WILD-TYPE  8 23 89 12
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                1                  8
  T2                6                 23
  T3               20                 89
  T4                2                 12
                    vv
clus                 N0 N1 N2
  17Q GAIN MUTATED   15  6  8
  17Q GAIN WILD-TYPE 68 39 24
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               15                 68
  N1                6                 39
  N2                8                 24
                    vv
clus                  M0  M1 M1A  MX
  17Q GAIN MUTATED    20   6   0   3
  17Q GAIN WILD-TYPE 103  16   2  10
D31V6, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                20                103
  M1                 6                 16
  M1A                0                  2
  MX                 3                 10
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   12 17
  17Q GAIN WILD-TYPE 62 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   17
  17Q GAIN WILD-TYPE   62   71
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               12                 62
  MALE                 17                 71
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    28   1
  17Q GAIN WILD-TYPE 115  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     28    1
  17Q GAIN WILD-TYPE  115   12
                                clus
vv                               17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        28                115
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  29
  17Q GAIN WILD-TYPE   6 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   29
  17Q GAIN WILD-TYPE    6  127
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  6
  YES               29                127
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED   22  0  3  0
  17Q GAIN WILD-TYPE 99  2  9  3
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               22                 99
  R1                0                  2
  R2                3                  9
  RX                0                  3
D31V11, continuous

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     3   1
  18P GAIN WILD-TYPE 114  12
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                126 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 12 
$`18P GAIN MUTATED`
TCGA-AF-6672 TCGA-AG-A01Y TCGA-AG-A02G TCGA-DT-5265 
       10.39        63.98        38.93         5.29 

$`18P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       11.67        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        10.98        51.98        49.94         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         6.97        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.41        41.33        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.58         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.37         8.61        11.51        10.78        13.61 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46        11.97         8.45         3.39         0.85         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              5.29               0.39 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             63.98             129.27 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            24.660             10.995 
[1] "5.3 - 64.0 (24.7)"  "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18P GAIN MUTATED         0        2         2         0         0         1
  18P GAIN WILD-TYPE      30        6        36         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18P GAIN MUTATED            0          0          2        2         0
  18P GAIN WILD-TYPE          9         23         12       15         9
D32V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED     0   1   6   2
  18P GAIN WILD-TYPE   9  28 103  12
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3                6                103
  T4                2                 12
                    vv
clus                 N0 N1 N2
  18P GAIN MUTATED    4  2  3
  18P GAIN WILD-TYPE 79 43 29
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                4                 79
  N1                2                 43
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  18P GAIN MUTATED     6   1   0   2
  18P GAIN WILD-TYPE 117  21   2  11
D32V6, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                 6                117
  M1                 1                 21
  M1A                0                  2
  MX                 2                 11
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  5
  18P GAIN WILD-TYPE 70 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    5
  18P GAIN WILD-TYPE   70   83
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  5                 83
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     7   2
  18P GAIN WILD-TYPE 136  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    2
  18P GAIN WILD-TYPE  136   11
                                clus
vv                               18P GAIN MUTATED 18P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         7                136
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1   8
  18P GAIN WILD-TYPE   5 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    8
  18P GAIN WILD-TYPE    5  148
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  5
  YES                8                148
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED     5   0   1   1
  18P GAIN WILD-TYPE 116   2  11   2
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                5                116
  R1                0                  2
  R2                1                 11
  RX                1                  2
D32V11, continuous

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     2   1
  18Q GAIN WILD-TYPE 115  12
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                127 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 12 
$`18Q GAIN MUTATED`
TCGA-AF-6672 TCGA-AG-A02G TCGA-DT-5265 
       10.39        38.93         5.29 

$`18Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       11.67        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.94         9.37         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       14.01        15.02        36.00         6.97        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.02        10.06       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.58         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.37         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.61        17.46        11.97         8.45         3.39         0.85 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        2.17         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76         0.46        18.25        55.76        47.08 
TCGA-G5-6641 
       26.43 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              5.29               0.39 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             38.93             129.27 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             10.39              11.01 
[1] "5.3 - 38.9 (10.4)"  "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18Q GAIN WILD-TYPE" 
[1] "hr=" "3.6"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18Q GAIN MUTATED         0        1         0         0         0         1
  18Q GAIN WILD-TYPE      30        7        38         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18Q GAIN MUTATED            0          0          2        2         0
  18Q GAIN WILD-TYPE          9         23         12       15         9
D33V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED     0   1   3   2
  18Q GAIN WILD-TYPE   9  28 106  12
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3                3                106
  T4                2                 12
                    vv
clus                 N0 N1 N2
  18Q GAIN MUTATED    1  2  3
  18Q GAIN WILD-TYPE 82 43 29
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                1                 82
  N1                2                 43
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  18Q GAIN MUTATED     3   1   0   2
  18Q GAIN WILD-TYPE 120  21   2  11
D33V6, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                 3                120
  M1                 1                 21
  M1A                0                  2
  MX                 2                 11
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  5
  18Q GAIN WILD-TYPE 73 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    5
  18Q GAIN WILD-TYPE   73   83
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 73
  MALE                  5                 83
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5   1
  18Q GAIN WILD-TYPE 138  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    1
  18Q GAIN WILD-TYPE  138   12
                                clus
vv                               18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         5                138
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   5
  18Q GAIN WILD-TYPE   5 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    5
  18Q GAIN WILD-TYPE    5  151
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                  5
  YES                5                151
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     2   0   1   1
  18Q GAIN WILD-TYPE 119   2  11   2
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                2                119
  R1                0                  2
  R2                1                 11
  RX                1                  2
D33V11, continuous

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   22  2
  19P GAIN WILD-TYPE 95 11
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                24                106 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 11 
$`19P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3878 TCGA-AG-3896 
       17.95        17.23         1.02         1.02         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 
        1.02         1.02        15.91        12.00        12.00         1.94 
TCGA-AG-A032 TCGA-CI-6619 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 
       38.01         6.02        10.98        11.01        12.00        36.00 
TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6863 
      129.27        20.55        17.69        16.31        13.61         0.76 

$`19P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       24.13        10.62        13.55        19.10        12.72        25.02 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.35        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 
       12.00         1.02         2.01         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 
        7.96         0.95         1.02         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4008 TCGA-AG-4022 
        1.02         0.99         0.99         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       13.02         1.02         1.02        70.03        63.98        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       51.98        49.94        38.93        61.94        40.96         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.94         9.37         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        15.02        12.99        14.01        15.02         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.02        10.06         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.33        57.24        24.13        51.48        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.37         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        1.02         0.66         0.69         0.53         1.08         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        55.76        47.08        26.43 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.76               0.39 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            129.27             126.41 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              12.0               10.7 
[1] "0.8 - 129.3 (12.0)" "0.4 - 126.4 (10.7)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "19P GAIN MUTATED"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19P GAIN MUTATED         7        1         5         0         0         1
  19P GAIN WILD-TYPE      23        7        33         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19P GAIN MUTATED            0          5          3        6         1
  19P GAIN WILD-TYPE          9         18         11       11         8
D34V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    0  8 17  4
  19P GAIN WILD-TYPE  9 21 92 10
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                0                  9
  T2                8                 21
  T3               17                 92
  T4                4                 10
                    vv
clus                 N0 N1 N2
  19P GAIN MUTATED   14  9  6
  19P GAIN WILD-TYPE 69 36 26
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               14                 69
  N1                9                 36
  N2                6                 26
                    vv
clus                  M0  M1 M1A  MX
  19P GAIN MUTATED    21   7   0   1
  19P GAIN WILD-TYPE 102  15   2  12
D34V6, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                21                102
  M1                 7                 15
  M1A                0                  2
  MX                 1                 12
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   15 14
  19P GAIN WILD-TYPE 59 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     15   14
  19P GAIN WILD-TYPE   59   74
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               15                 59
  MALE                 14                 74
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    29   0
  19P GAIN WILD-TYPE 114  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     29    0
  19P GAIN WILD-TYPE  114   13
                                clus
vv                               19P GAIN MUTATED 19P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        29                114
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  29
  19P GAIN WILD-TYPE   6 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   29
  19P GAIN WILD-TYPE    6  127
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 0                  6
  YES               29                127
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED   22  1  3  0
  19P GAIN WILD-TYPE 99  1  9  3
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               22                 99
  R1                1                  1
  R2                3                  9
  RX                0                  3
D34V11, continuous

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   23  1
  19Q GAIN WILD-TYPE 94 12
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                106 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 12 
$`19Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AG-3587 TCGA-AG-3878 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A014 
       17.95         1.02         0.99         1.02         1.02        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 
       13.02         1.02        12.00        12.00         1.94        38.01 
TCGA-CI-6619 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 
        6.02        13.97        10.98        11.01        12.00        36.00 
TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6863 
      129.27        20.55        17.69        16.31        13.61         0.76 

$`19Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       10.39        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         0.99        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       25.94        23.01        17.03         1.02        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        51.98        49.94        38.93        61.94        40.96 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       10.19         6.02         6.94         9.37         4.70        60.00 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        15.02        12.99        14.01        15.02         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.02        10.06         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.33        57.24        24.13        51.48        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.37         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        1.02         0.66         0.69         0.53         1.08         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        55.76        47.08        26.43 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.76               0.39 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            129.27             126.41 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            12.000             10.505 
[1] "0.8 - 129.3 (12.0)" "0.4 - 126.4 (10.5)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19Q GAIN MUTATED         8        1         5         0         0         1
  19Q GAIN WILD-TYPE      22        7        33         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19Q GAIN MUTATED            1          6          1        6         1
  19Q GAIN WILD-TYPE          8         17         13       11         8
D35V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED    1  8 16  5
  19Q GAIN WILD-TYPE  8 21 93  9
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                1                  8
  T2                8                 21
  T3               16                 93
  T4                5                  9
                    vv
clus                 N0 N1 N2
  19Q GAIN MUTATED   15 10  5
  19Q GAIN WILD-TYPE 68 35 27
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               15                 68
  N1               10                 35
  N2                5                 27
                    vv
clus                  M0  M1 M1A  MX
  19Q GAIN MUTATED    22   7   0   1
  19Q GAIN WILD-TYPE 101  15   2  12
D35V6, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                22                101
  M1                 7                 15
  M1A                0                  2
  MX                 1                 12
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   16 14
  19Q GAIN WILD-TYPE 58 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     16   14
  19Q GAIN WILD-TYPE   58   74
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               16                 58
  MALE                 14                 74
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    30   0
  19Q GAIN WILD-TYPE 113  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     30    0
  19Q GAIN WILD-TYPE  113   13
                                clus
vv                               19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        30                113
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0  30
  19Q GAIN WILD-TYPE   6 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   30
  19Q GAIN WILD-TYPE    6  126
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 0                  6
  YES               30                126
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    21   1   4   0
  19Q GAIN WILD-TYPE 100   1   8   3
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               21                100
  R1                1                  1
  R2                4                  8
  RX                0                  3
D35V11, continuous

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   76  8
  20P GAIN WILD-TYPE 41  5
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                84                 46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                  5 
$`20P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        19.10        25.02        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        8.45        11.67        10.39         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        1.02         1.02         0.99         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.99         1.02         0.92         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02         1.02         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 
       17.03        13.02         1.02        51.98        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.02         6.94         9.37         4.70        13.97 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98        15.02        12.99        12.00        14.01        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE 
       36.00         6.97        30.05        12.95       126.41       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       24.13        32.58         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
       18.28        15.85        17.69        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       13.61        11.97         3.39         0.39         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.08         0.76        18.25        55.76        47.08 

$`20P GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3575 
       10.62        13.55        12.72        14.50        15.35        12.00 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-4022 TCGA-AG-A002 
        0.99         7.96         1.02         0.99         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       13.91        15.91         1.02        12.00        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       63.98        10.98        49.94         1.94        38.93        61.94 
TCGA-CI-6620 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6682 TCGA-DC-6683 
        6.02        60.00         7.99        11.01        13.02        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6507 
        5.29        41.33        57.24        51.48         0.49        19.96 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 
       16.34        16.37         8.61        17.46         8.45         0.85 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6641 
        2.17         0.69         0.46        26.43 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.39               0.46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            129.27              70.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             10.39              12.00 
[1] "0.4 - 129.3 (10.4)" "0.5 - 70.0 (12.0)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-G5-6641 
"20P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-G5-6641 
"20P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-G5-6641 
"20P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20P GAIN MUTATED        20        0        24         1         2         4
  20P GAIN WILD-TYPE      10        8        14         1         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20P GAIN MUTATED            6         15          9       13         4
  20P GAIN WILD-TYPE          3          8          5        4         5
D36V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    5 20 69  8
  20P GAIN WILD-TYPE  4  9 40  6
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                5                  4
  T2               20                  9
  T3               69                 40
  T4                8                  6
                    vv
clus                 N0 N1 N2
  20P GAIN MUTATED   49 28 24
  20P GAIN WILD-TYPE 34 17  8
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               49                 34
  N1               28                 17
  N2               24                  8
                    vv
clus                 M0 M1 M1A MX
  20P GAIN MUTATED   76 15   2  8
  20P GAIN WILD-TYPE 47  7   0  5
D36V6, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                76                 47
  M1                15                  7
  M1A                2                  0
  MX                 8                  5
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   43 60
  20P GAIN WILD-TYPE 31 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     43   60
  20P GAIN WILD-TYPE   31   28
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               43                 31
  MALE                 60                 28
D36V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   96  4
  20P GAIN WILD-TYPE 47  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     96    4
  20P GAIN WILD-TYPE   47    9
                                clus
vv                               20P GAIN MUTATED 20P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        96                 47
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
D36V9, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    4 99
  20P GAIN WILD-TYPE  2 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   99
  20P GAIN WILD-TYPE    2   57
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 4                  2
  YES               99                 57
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   77  1  7  0
  20P GAIN WILD-TYPE 44  1  5  3
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               77                 44
  R1                1                  1
  R2                7                  5
  RX                0                  3
D36V11, continuous

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   103  13
  20Q GAIN WILD-TYPE  14   0
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               116                 14 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                  0 
$`20Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       24.13        17.95        17.23        10.62        19.10        25.02 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.35        11.67        10.39 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        1.02         0.92         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         1.02         0.99        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.94        23.01        17.03        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        12.00        70.03        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.93        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        6.02         6.94         9.37         4.70        13.97         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         6.97        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.41        41.33        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       51.48        32.58         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 
       16.37        11.51        10.78        13.61        11.97         3.39 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        0.85         2.17         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.08         0.76         0.46        18.25        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`20Q GAIN WILD-TYPE`
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A01Y 
       13.55        12.72        12.00         1.02        20.94        63.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-CL-5917 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 
       49.94        61.94        60.00         5.29        19.96         8.61 
TCGA-EI-6917 TCGA-EI-7004 
       17.46         8.45 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.39               1.02 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            129.27              63.98 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            10.700             15.505 
[1] "0.4 - 129.3 (10.7)" "1.0 - 64.0 (15.5)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6641 
  "20Q GAIN MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6641 
  "20Q GAIN MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6641 
  "20Q GAIN MUTATED" 
[1] "hr="     "3.1e+08"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20Q GAIN MUTATED        26        4        31         2         2         5
  20Q GAIN WILD-TYPE       4        4         7         0         0         0
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20Q GAIN MUTATED            8         23         12       16         8
  20Q GAIN WILD-TYPE          1          0          2        1         1
D37V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    7 27 94 13
  20Q GAIN WILD-TYPE  2  2 15  1
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                7                  2
  T2               27                  2
  T3               94                 15
  T4               13                  1
                    vv
clus                 N0 N1 N2
  20Q GAIN MUTATED   68 44 28
  20Q GAIN WILD-TYPE 15  1  4
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               68                 15
  N1               44                  1
  N2               28                  4
                    vv
clus                  M0  M1 M1A  MX
  20Q GAIN MUTATED   105  21   2  12
  20Q GAIN WILD-TYPE  18   1   0   1
D37V6, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               105                 18
  M1                21                  1
  M1A                2                  0
  MX                12                  1
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   64 78
  20Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     64   78
  20Q GAIN WILD-TYPE   10   10
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               64                 10
  MALE                 78                 10
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   131   7
  20Q GAIN WILD-TYPE  12   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    131    7
  20Q GAIN WILD-TYPE   12    6
                                clus
vv                               20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       131                 12
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     5 137
  20Q GAIN WILD-TYPE   1  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5  137
  20Q GAIN WILD-TYPE    1   19
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 5                  1
  YES              137                 19
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   105   2  11   1
  20Q GAIN WILD-TYPE  16   0   1   2
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              105                 16
  R1                2                  0
  R2               11                  1
  RX                1                  2
D37V11, continuous

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     5   0
  21Q GAIN WILD-TYPE 112  13
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                125 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                 13 
$`21Q GAIN MUTATED`
TCGA-AG-A011 TCGA-AH-6644 TCGA-CI-6623 TCGA-EF-5830 TCGA-EI-6885 
       17.03         0.72         9.37         0.49        13.61 

$`21Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.02         6.94         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         6.97        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.58         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.37         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.25        55.76        47.08        26.43 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.49               0.39 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             17.03             129.27 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              9.37              11.01 
[1] "0.5 - 17.0 (9.4)"   "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"21Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"21Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"21Q GAIN WILD-TYPE" 
[1] "hr="     "9400000"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  21Q GAIN MUTATED         2        0         2         1         0         0
  21Q GAIN WILD-TYPE      28        8        36         1         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  21Q GAIN MUTATED            0          2          0        2         0
  21Q GAIN WILD-TYPE          9         21         14       15         9
D38V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED     1   1   7   1
  21Q GAIN WILD-TYPE   8  28 102  13
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                1                  8
  T2                1                 28
  T3                7                102
  T4                1                 13
                    vv
clus                 N0 N1 N2
  21Q GAIN MUTATED    5  3  1
  21Q GAIN WILD-TYPE 78 42 31
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                5                 78
  N1                3                 42
  N2                1                 31
                    vv
clus                  M0  M1 M1A  MX
  21Q GAIN MUTATED     7   2   0   1
  21Q GAIN WILD-TYPE 116  20   2  12
D38V6, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                 7                116
  M1                 2                 20
  M1A                0                  2
  MX                 1                 12
D38V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5  5
  21Q GAIN WILD-TYPE 69 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    5
  21Q GAIN WILD-TYPE   69   83
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                5                 69
  MALE                  5                 83
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    10   0
  21Q GAIN WILD-TYPE 133  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    0
  21Q GAIN WILD-TYPE  133   13
                                clus
vv                               21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        10                133
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  10
  21Q GAIN WILD-TYPE   6 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   10
  21Q GAIN WILD-TYPE    6  146
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  6
  YES               10                146
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED     7   0   1   0
  21Q GAIN WILD-TYPE 114   2  11   3
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                7                114
  R1                0                  2
  R2                1                 11
  RX                0                  3
D38V11, continuous

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     5   2
  22Q GAIN WILD-TYPE 112  11
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                123 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 2                 11 
$`22Q GAIN MUTATED`
TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3893 TCGA-AG-A00Y TCGA-AH-6897 TCGA-CI-6623 
       17.23         1.02         0.99        23.01         4.60         9.37 
TCGA-DY-A1DF 
       24.13 

$`22Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       10.39        12.00         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        0.99         1.02         0.92         1.02         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
        1.02         1.02         1.02         1.02         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.91         6.02        25.94        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        1.02         1.02        12.00        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       40.96        38.01         0.49         1.45         0.69         0.72 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        1.81        10.19         6.02         6.02         6.94         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        14.01        15.02        36.00         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.02        10.06         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.33        57.24       129.27        51.48        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.37         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.61        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        3.39         0.85         2.17         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.08         0.76         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.99               0.39 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             24.13             129.27 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              9.37              11.01 
[1] "1.0 - 24.1 (9.4)"   "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"22Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"22Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"22Q GAIN WILD-TYPE" 
[1] "hr=" "8.6"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  22Q GAIN MUTATED         2        0         1         0         0         0
  22Q GAIN WILD-TYPE      28        8        37         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  22Q GAIN MUTATED            0          2          3        1         0
  22Q GAIN WILD-TYPE          9         21         11       16         9
D39V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED     1   1   7   0
  22Q GAIN WILD-TYPE   8  28 102  14
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                1                  8
  T2                1                 28
  T3                7                102
  T4                0                 14
                    vv
clus                 N0 N1 N2
  22Q GAIN MUTATED    3  3  3
  22Q GAIN WILD-TYPE 80 42 29
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                3                 80
  N1                3                 42
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  22Q GAIN MUTATED     8   1   0   0
  22Q GAIN WILD-TYPE 115  21   2  13
D39V6, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                 8                115
  M1                 1                 21
  M1A                0                  2
  MX                 0                 13
D39V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  5
  22Q GAIN WILD-TYPE 70 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    5
  22Q GAIN WILD-TYPE   70   83
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  5                 83
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     9   0
  22Q GAIN WILD-TYPE 134  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      9    0
  22Q GAIN WILD-TYPE  134   13
                                clus
vv                               22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         9                134
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   9
  22Q GAIN WILD-TYPE   6 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    9
  22Q GAIN WILD-TYPE    6  147
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  6
  YES                9                147
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED     6   0   1   0
  22Q GAIN WILD-TYPE 115   2  11   3
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                6                115
  R1                0                  2
  R2                1                 11
  RX                0                  3
D39V11, continuous

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   24  2
  XQ GAIN WILD-TYPE 93 11
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               26               104 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                11 
$`XQ GAIN MUTATED`
TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3893 TCGA-AG-3896 
       13.55        10.39         8.45        11.67         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        1.02         1.02         0.99        15.91        13.02         1.02 
TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 
       38.01         0.72         9.37        60.00        10.98        12.00 
TCGA-DC-6156 TCGA-DY-A1DD TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-F5-6465 
       15.02        57.24        18.28        17.69        13.61         3.39 
TCGA-F5-6810 TCGA-F5-6863 
        0.39         0.76 

$`XQ GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        10.62        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 
       25.02        14.50        15.35        10.39        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        7.96         0.95         1.02         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 
        0.92         1.02         0.99         1.02         1.02        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       13.91         6.02        25.94        23.01        17.03         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.94         1.94        38.93        61.94        40.96         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
        6.02         6.94         4.70        13.97         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        14.01        36.00         6.97        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.02        10.06         5.29       126.41        41.33 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.58         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
       20.55        19.96        20.91        17.00        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.37         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         0.85         2.17         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.08         0.46        18.25        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.39              0.46 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            60.00            129.27 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           10.685            11.260 
[1] "0.4 - 60.0 (10.7)"  "0.5 - 129.3 (11.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XQ GAIN MUTATED         5        2         6         0         0         0
  XQ GAIN WILD-TYPE      25        6        32         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XQ GAIN MUTATED            1          8          4        3         3
  XQ GAIN WILD-TYPE          8         15         10       14         6
D40V3, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED    2  5 21  6
  XQ GAIN WILD-TYPE  7 24 88  8
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2                 7
  T2               5                24
  T3              21                88
  T4               6                 8
                   vv
clus                N0 N1 N2
  XQ GAIN MUTATED   14 11  8
  XQ GAIN WILD-TYPE 69 34 24
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              14                69
  N1              11                34
  N2               8                24
                   vv
clus                M0 M1 M1A MX
  XQ GAIN MUTATED   25  5   1  3
  XQ GAIN WILD-TYPE 98 17   1 10
D40V6, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               25                98
  M1                5                17
  M1A               1                 1
  MX                3                10
D40V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   20 14
  XQ GAIN WILD-TYPE 54 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     20   14
  XQ GAIN WILD-TYPE   54   74
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              20                54
  MALE                14                74
D40V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    31   1
  XQ GAIN WILD-TYPE 112  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     31    1
  XQ GAIN WILD-TYPE  112   12
                                clus
vv                               XQ GAIN MUTATED XQ GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       31               112
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D40V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  34
  XQ GAIN WILD-TYPE   6 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   34
  XQ GAIN WILD-TYPE    6  122
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 6
  YES              34               122
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED   26  0  3  1
  XQ GAIN WILD-TYPE 95  2  9  2
D40V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              26                95
  R1               0                 2
  R2               3                 9
  RX               1                 2
D40V11, continuous

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   31  3
  1P LOSS WILD-TYPE 86 10
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34                96 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                10 
$`1P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3731 
       24.13        17.23        14.50        15.35         1.02         1.02 
TCGA-AG-3883 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
        1.02         1.02         1.02        25.94        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 
       70.03        38.93         0.49         0.69        10.19         9.37 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 
        4.70        11.01        12.99        14.01        36.00        30.05 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 
      126.41       129.27         0.49        20.55        15.85        11.97 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
        2.17         1.02         0.69        47.08 

$`1P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        10.62        13.55        19.10        12.72        25.02 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 
       10.39         8.45        11.67        10.39        12.00         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        2.01         1.02         1.02         0.99         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.95         0.99         0.99         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
        0.99         1.02         1.02         1.02         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.91         6.02        17.03        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
        1.94        61.94        40.96        38.01         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        4.60         1.81         6.02         6.02         6.94        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
       60.00         7.99        10.98        15.02        12.00        15.02 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
        6.97        12.95        13.02        10.06         5.29        41.33 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 
       57.24        24.13        51.48        32.58         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.37         8.61        11.51        10.78        13.61        17.46 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 
        8.45         3.39         0.85         0.39         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        1.08         0.76         0.46        18.25        55.76        26.43 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.49              0.39 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.27             63.98 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           12.495            10.700 
[1] "0.5 - 129.3 (12.5)" "0.4 - 64.0 (10.7)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1P LOSS MUTATED         7        1        10         1         0         1
  1P LOSS WILD-TYPE      23        7        28         1         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1P LOSS MUTATED            1          7          5        5         2
  1P LOSS WILD-TYPE          8         16          9       12         7
D41V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    1  8 29  3
  1P LOSS WILD-TYPE  8 21 80 11
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               1                 8
  T2               8                21
  T3              29                80
  T4               3                11
                   vv
clus                N0 N1 N2
  1P LOSS MUTATED   19 14  8
  1P LOSS WILD-TYPE 64 31 24
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              19                64
  N1              14                31
  N2               8                24
                   vv
clus                M0 M1 M1A MX
  1P LOSS MUTATED   30  7   0  3
  1P LOSS WILD-TYPE 93 15   2 10
D41V6, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               30                93
  M1                7                15
  M1A               0                 2
  MX                3                10
D41V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   16 26
  1P LOSS WILD-TYPE 58 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     16   26
  1P LOSS WILD-TYPE   58   62
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              16                58
  MALE                26                62
D41V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    40   0
  1P LOSS WILD-TYPE 103  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     40    0
  1P LOSS WILD-TYPE  103   13
                                clus
vv                               1P LOSS MUTATED 1P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       40               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D41V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3  39
  1P LOSS WILD-TYPE   3 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3   39
  1P LOSS WILD-TYPE    3  117
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3                 3
  YES              39               117
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   28  0  4  0
  1P LOSS WILD-TYPE 93  2  8  3
D41V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              28                93
  R1               0                 2
  R2               4                 8
  RX               0                 3
D41V11, continuous

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   19  1
  1Q LOSS WILD-TYPE 98 12
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20               110 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                12 
$`1Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3731 TCGA-AG-3883 
       24.13        14.50        15.35         1.02         1.02         1.02 
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A01L TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-4749 
        1.02        25.94        12.00        10.19         4.70        11.01 
TCGA-DC-5869 TCGA-DC-6157 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 
       12.99        36.00         0.49        20.55        15.85        11.97 
TCGA-F5-6702 TCGA-G5-6572 
        2.17        47.08 

$`1Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       25.02        10.39         8.45        11.67        10.39        12.00 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 
        7.96         0.95         0.99         0.99         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.94        13.91         6.02        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       15.91        13.02         1.02         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        9.37        13.97        60.00         7.99        10.98        15.02 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.00        14.01        15.02         6.97        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.02        10.06         5.29       126.41        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 
      129.27        24.13        51.48        32.58         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.37         8.61        11.51        10.78        13.61        17.46 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45         3.39         0.85         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.08         0.76         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.49              0.39 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            47.08            129.27 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           11.985            10.880 
[1] "0.5 - 47.1 (12.0)"  "0.4 - 129.3 (10.9)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1Q LOSS MUTATED         5        0         3         1         0         1
  1Q LOSS WILD-TYPE      25        8        35         1         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1Q LOSS MUTATED            0          6          1        4         2
  1Q LOSS WILD-TYPE          9         17         13       13         7
D42V3, multiclass
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    0  5 16  2
  1Q LOSS WILD-TYPE  9 24 93 12
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0                 9
  T2               5                24
  T3              16                93
  T4               2                12
                   vv
clus                N0 N1 N2
  1Q LOSS MUTATED    9 10  4
  1Q LOSS WILD-TYPE 74 35 28
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               9                74
  N1              10                35
  N2               4                28
                   vv
clus                 M0  M1 M1A  MX
  1Q LOSS MUTATED    14   5   0   3
  1Q LOSS WILD-TYPE 109  17   2  10
D42V6, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               14               109
  M1                5                17
  M1A               0                 2
  MX                3                10
D42V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    7 17
  1Q LOSS WILD-TYPE 67 71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7   17
  1Q LOSS WILD-TYPE   67   71
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               7                67
  MALE                17                71
D42V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    23   0
  1Q LOSS WILD-TYPE 120  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     23    0
  1Q LOSS WILD-TYPE  120   13
                                clus
vv                               1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       23               120
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D42V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  21
  1Q LOSS WILD-TYPE   3 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   21
  1Q LOSS WILD-TYPE    3  135
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                 3
  YES              21               135
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    17   0   3   0
  1Q LOSS WILD-TYPE 104   2   9   3
D42V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              17               104
  R1               0                 2
  R2               3                 9
  RX               0                 3
D42V11, continuous

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     8   0
  2P LOSS WILD-TYPE 109  13
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8               122 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                13 
$`2P LOSS MUTATED`
TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A02X 
       15.35         1.02         1.02         1.02        25.94        40.96 
TCGA-EF-5831 TCGA-F5-6571 
        2.40         0.85 

$`2P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       12.72        25.02        10.39        14.50         8.45        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       10.39        12.00         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        23.01        17.03        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        12.00        70.03        63.98        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.94         1.94        38.93        61.94        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.02         6.02         6.94         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        14.01        15.02        36.00         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.02        10.06         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.33        57.24       129.27        24.13        51.48        32.58 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.37         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.61        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        3.39         2.17         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.08         0.76         0.46        18.25        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.85              0.39 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            40.96            129.27 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.71             11.26 
[1] "0.8 - 41.0 (1.7)"   "0.4 - 129.3 (11.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2P LOSS MUTATED         1        0         7         0         0         0
  2P LOSS WILD-TYPE      29        8        31         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2P LOSS MUTATED            0          1          1        1         0
  2P LOSS WILD-TYPE          9         22         13       16         9
D43V3, multiclass
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    0  1 10  0
  2P LOSS WILD-TYPE  9 28 99 14
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                 9
  T2               1                28
  T3              10                99
  T4               0                14
                   vv
clus                N0 N1 N2
  2P LOSS MUTATED    8  2  1
  2P LOSS WILD-TYPE 75 43 31
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               8                75
  N1               2                43
  N2               1                31
                   vv
clus                 M0  M1 M1A  MX
  2P LOSS MUTATED     9   1   0   1
  2P LOSS WILD-TYPE 114  21   2  12
D43V6, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0                9               114
  M1                1                21
  M1A               0                 2
  MX                1                12
D43V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  5
  2P LOSS WILD-TYPE 68 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    5
  2P LOSS WILD-TYPE   68   83
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               6                68
  MALE                 5                83
D43V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   1
  2P LOSS WILD-TYPE 134  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    1
  2P LOSS WILD-TYPE  134   12
                                clus
vv                               2P LOSS MUTATED 2P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        9               134
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D43V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  10
  2P LOSS WILD-TYPE   5 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   10
  2P LOSS WILD-TYPE    5  146
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                 5
  YES              10               146
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     8   0   1   0
  2P LOSS WILD-TYPE 113   2  11   3
D43V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               8               113
  R1               0                 2
  R2               1                11
  RX               0                 3
D43V11, continuous

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED     4   0
  2Q LOSS WILD-TYPE 113  13
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4               126 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                13 
$`2Q LOSS MUTATED`
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A02X TCGA-F5-6571 
        1.02        25.94        40.96         0.85 

$`2Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.94        13.91         6.02        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        63.98        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.93        61.94        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         6.97        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.58         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.37         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6702 
       13.61        17.46        11.97         8.45         3.39         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.85              0.39 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            40.96            129.27 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           13.480            10.995 
[1] "0.8 - 41.0 (13.5)"  "0.4 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2Q LOSS MUTATED         1        0         5         0         0         0
  2Q LOSS WILD-TYPE      29        8        33         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2Q LOSS MUTATED            0          0          0        0         0
  2Q LOSS WILD-TYPE          9         23         14       17         9
D44V3, multiclass
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     0   1   5   0
  2Q LOSS WILD-TYPE   9  28 104  14
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                 9
  T2               1                28
  T3               5               104
  T4               0                14
                   vv
clus                N0 N1 N2
  2Q LOSS MUTATED    6  0  0
  2Q LOSS WILD-TYPE 77 45 32
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               6                77
  N1               0                45
  N2               0                32
                   vv
clus                 M0  M1 M1A  MX
  2Q LOSS MUTATED     6   0   0   0
  2Q LOSS WILD-TYPE 117  22   2  13
D44V6, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0                6               117
  M1                0                22
  M1A               0                 2
  MX                0                13
D44V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3  3
  2Q LOSS WILD-TYPE 71 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    3
  2Q LOSS WILD-TYPE   71   85
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                71
  MALE                 3                85
D44V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   0
  2Q LOSS WILD-TYPE 138  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    0
  2Q LOSS WILD-TYPE  138   13
                                clus
vv                               2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               138
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D44V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   6
  2Q LOSS WILD-TYPE   6 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    6
  2Q LOSS WILD-TYPE    6  150
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                 6
  YES               6               150
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     5   0   0   0
  2Q LOSS WILD-TYPE 116   2  12   3
D44V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               5               116
  R1               0                 2
  R2               0                12
  RX               0                 3
D44V11, continuous

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    10   1
  3P LOSS WILD-TYPE 107  12
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               11               119 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                12 
$`3P LOSS MUTATED`
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-3731 TCGA-AH-6544 TCGA-BM-6198 
       12.72        14.50         2.01         1.02         0.49        10.19 
TCGA-CI-6619 TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6810 TCGA-G5-6233 
        6.02        13.02         5.29         0.39        18.25 

$`3P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       25.02        10.39         8.45        15.35        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
       12.00         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99         7.96         0.95         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        1.02         1.02        12.00        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       40.96        38.01         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        1.81         6.02         6.94         9.37         4.70        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.00         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        14.01        15.02        36.00         6.97        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       12.95        10.06       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.58         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.37         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.61        17.46        11.97         8.45         3.39         0.85 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        2.17         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.39              0.46 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            18.25            129.27 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             6.02             11.51 
[1] "0.4 - 18.2 (6.0)"   "0.5 - 129.3 (11.5)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "4.6"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3P LOSS MUTATED         0        1         4         0         1         0
  3P LOSS WILD-TYPE      30        7        34         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3P LOSS MUTATED            0          2          0        5         1
  3P LOSS WILD-TYPE          9         21         14       12         8
D45V3, multiclass
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    0  0 14  1
  3P LOSS WILD-TYPE  9 29 95 13
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               0                 9
  T2               0                29
  T3              14                95
  T4               1                13
                   vv
clus                N0 N1 N2
  3P LOSS MUTATED    5  5  5
  3P LOSS WILD-TYPE 78 40 27
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               5                78
  N1               5                40
  N2               5                27
                   vv
clus                 M0  M1 M1A  MX
  3P LOSS MUTATED     7   6   0   1
  3P LOSS WILD-TYPE 116  16   2  12
D45V6, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0                7               116
  M1                6                16
  M1A               0                 2
  MX                1                12
D45V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3 12
  3P LOSS WILD-TYPE 71 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3   12
  3P LOSS WILD-TYPE   71   76
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               3                71
  MALE                12                76
D45V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    10   3
  3P LOSS WILD-TYPE 133  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    3
  3P LOSS WILD-TYPE  133   10
                                clus
vv                               3P LOSS MUTATED 3P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       10               133
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
D45V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2  13
  3P LOSS WILD-TYPE   4 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   13
  3P LOSS WILD-TYPE    4  143
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                2                 4
  YES              13               143
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED     7   0   4   1
  3P LOSS WILD-TYPE 114   2   8   2
D45V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               7               114
  R1               0                 2
  R2               4                 8
  RX               1                 2
D45V11, continuous

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   1
  3Q LOSS WILD-TYPE 110  12
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8               122 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                12 
$`3Q LOSS MUTATED`
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-3731 TCGA-BM-6198 TCGA-CI-6619 
       12.72        14.50         2.01         1.02        10.19         6.02 
TCGA-DT-5265 TCGA-G5-6233 
        5.29        18.25 

$`3Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       25.02        10.39         8.45        15.35        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
       12.00         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99         7.96         0.95         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        1.02         1.02        12.00        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       40.96        38.01         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        4.60         1.81         6.02         6.94         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        14.01        15.02        36.00         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.02        10.06       126.41        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.37         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.61        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        3.39         0.85         2.17         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.08         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.02              0.39 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            18.25            129.27 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            8.105            11.260 
[1] "1.0 - 18.2 (8.1)"   "0.4 - 129.3 (11.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "5.4"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3Q LOSS MUTATED         0        1         2         0         1         0
  3Q LOSS WILD-TYPE      30        7        36         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3Q LOSS MUTATED            0          1          0        4         1
  3Q LOSS WILD-TYPE          9         22         14       13         8
D46V3, multiclass
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     0   0   9   1
  3Q LOSS WILD-TYPE   9  29 100  13
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                 9
  T2               0                29
  T3               9               100
  T4               1                13
                   vv
clus                N0 N1 N2
  3Q LOSS MUTATED    3  3  4
  3Q LOSS WILD-TYPE 80 42 28
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               3                80
  N1               3                42
  N2               4                28
                   vv
clus                 M0  M1 M1A  MX
  3Q LOSS MUTATED     4   4   0   1
  3Q LOSS WILD-TYPE 119  18   2  12
D46V6, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0                4               119
  M1                4                18
  M1A               0                 2
  MX                1                12
D46V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  8
  3Q LOSS WILD-TYPE 72 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    8
  3Q LOSS WILD-TYPE   72   80
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                72
  MALE                 8                80
D46V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5   4
  3Q LOSS WILD-TYPE 138   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    4
  3Q LOSS WILD-TYPE  138    9
                                clus
vv                               3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               138
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
D46V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   8
  3Q LOSS WILD-TYPE   4 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    8
  3Q LOSS WILD-TYPE    4  148
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                2                 4
  YES               8               148
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED     5   0   3   1
  3Q LOSS WILD-TYPE 116   2   9   2
D46V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               5               116
  R1               0                 2
  R2               3                 9
  RX               1                 2
D46V11, continuous

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   39  3
  4P LOSS WILD-TYPE 78 10
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               42                88 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                10 
$`4P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       24.13        17.23        10.62        12.72        25.02        14.50 
TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3999 
       15.35         1.02         1.02         1.02         0.99         1.02 
TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
        1.02        13.91        25.94        23.01        12.00        70.03 
TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       40.96         0.69        10.19         6.02         6.02         4.70 
TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA 
       12.99        15.02        36.00         6.97        30.05       126.41 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
      129.27        32.58         2.40        15.85        16.34        16.37 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-G5-6641 
       11.97         0.85         2.17         0.39         0.69        26.43 

$`4P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       17.95        13.55        19.10        10.39         8.45        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       10.39        12.00         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
        0.99         0.99         7.96         0.95         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4008 
        0.92         1.02         0.99         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.94         6.02        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02         1.02        12.00        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.94         1.94        38.93        61.94        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 
        1.45         0.72         4.60         1.81         6.94         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       12.00        14.01        12.95        13.02        10.06         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.33        57.24        24.13        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.61        17.46         8.45 
TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        3.39         1.02         0.66         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.46        18.25        55.76        47.08 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.39              0.46 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           129.27             63.98 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           12.855            10.585 
[1] "0.4 - 129.3 (12.9)" "0.5 - 64.0 (10.6)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "4P LOSS MUTATED"   "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
[1] "hr=" "1.7"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4P LOSS MUTATED         9        1        16         0         0         1
  4P LOSS WILD-TYPE      21        7        22         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4P LOSS MUTATED            3         11          7        5         4
  4P LOSS WILD-TYPE          6         12          7       12         5
D47V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    2  9 43  3
  4P LOSS WILD-TYPE  7 20 66 11
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               2                 7
  T2               9                20
  T3              43                66
  T4               3                11
                   vv
clus                N0 N1 N2
  4P LOSS MUTATED   26 19 12
  4P LOSS WILD-TYPE 57 26 20
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              26                57
  N1              19                26
  N2              12                20
                   vv
clus                M0 M1 M1A MX
  4P LOSS MUTATED   44  7   1  4
  4P LOSS WILD-TYPE 79 15   1  9
D47V6, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               44                79
  M1                7                15
  M1A               1                 1
  MX                4                 9
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   23 34
  4P LOSS WILD-TYPE 51 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     23   34
  4P LOSS WILD-TYPE   51   54
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              23                51
  MALE                34                54
D47V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   52  3
  4P LOSS WILD-TYPE 91 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     52    3
  4P LOSS WILD-TYPE   91   10
                                clus
vv                               4P LOSS MUTATED 4P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       52                91
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
D47V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5  52
  4P LOSS WILD-TYPE   1 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5   52
  4P LOSS WILD-TYPE    1  104
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                5                 1
  YES              52               104
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED   46  0  2  0
  4P LOSS WILD-TYPE 75  2 10  3
D47V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              46                75
  R1               0                 2
  R2               2                10
  RX               0                 3
D47V11, continuous

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   45  3
  4Q LOSS WILD-TYPE 72 10
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               48                82 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                10 
$`4Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3883 TCGA-AG-3999 
       25.02        14.50        15.35         1.02         1.02         1.02 
TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
        1.02        13.91        25.94        23.01        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       63.98        40.96         0.49         0.69        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 
        6.02         4.70        11.01        12.99        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
        6.97        30.05       126.41       129.27        32.58         2.40 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 
       17.00        15.85        16.34        16.37        11.97         0.85 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        2.17         0.39         1.02         0.66         0.69        26.43 

$`4Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       17.95        10.39         8.45        11.67        10.39        12.00 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        7.96         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4008 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.94         6.02        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02         1.02        12.00        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
        1.94        38.93        61.94        38.01         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        4.60         1.81         6.94         9.37        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 
        7.99        10.98        15.02        12.00        14.01        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.02        10.06         5.29        41.33        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         0.49        20.55        19.96        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.31         8.61        11.51        10.78        13.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       17.46         8.45         3.39         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.46        18.25        55.76        47.08 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.39              0.46 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           129.27             61.94 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           13.270            10.225 
[1] "0.4 - 129.3 (13.3)" "0.5 - 61.9 (10.2)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
[1] "hr=" "2.4"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4Q LOSS MUTATED        11        2        19         0         0         2
  4Q LOSS WILD-TYPE      19        6        19         2         2         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4Q LOSS MUTATED            3         11          8        4         4
  4Q LOSS WILD-TYPE          6         12          6       13         5
D48V3, multiclass
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    2 11 48  4
  4Q LOSS WILD-TYPE  7 18 61 10
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               2                 7
  T2              11                18
  T3              48                61
  T4               4                10
                   vv
clus                N0 N1 N2
  4Q LOSS MUTATED   32 20 13
  4Q LOSS WILD-TYPE 51 25 19
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              32                51
  N1              20                25
  N2              13                19
                   vv
clus                M0 M1 M1A MX
  4Q LOSS MUTATED   50  7   1  6
  4Q LOSS WILD-TYPE 73 15   1  7
D48V6, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               50                73
  M1                7                15
  M1A               1                 1
  MX                6                 7
D48V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   26 39
  4Q LOSS WILD-TYPE 48 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     26   39
  4Q LOSS WILD-TYPE   48   49
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              26                48
  MALE                39                49
D48V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   58  3
  4Q LOSS WILD-TYPE 85 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     58    3
  4Q LOSS WILD-TYPE   85   10
                                clus
vv                               4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       58                85
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
D48V9, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    5 60
  4Q LOSS WILD-TYPE  1 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5   60
  4Q LOSS WILD-TYPE    1   96
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                5                 1
  YES              60                96
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   50  0  2  0
  4Q LOSS WILD-TYPE 71  2 10  3
D48V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              50                71
  R1               0                 2
  R2               2                10
  RX               0                 3
D48V11, continuous

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    15   2
  5P LOSS WILD-TYPE 102  11
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               17               113 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                11 
$`5P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-6136 TCGA-AG-3731 TCGA-AG-3999 TCGA-AG-A00Y 
       24.13        10.62        15.35         1.02         1.02        23.01 
TCGA-AG-A01W TCGA-AG-A026 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A0XA 
       70.03         1.94         6.02        14.01        36.00       126.41 
TCGA-DY-A1DD TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7004 
       57.24        20.55        16.37        13.61         8.45 

$`5P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        13.55        19.10        12.72        25.02 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       10.39        14.50         8.45        11.67        10.39        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99         7.96         0.95         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         0.99        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.94        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        12.00        63.98        10.98        51.98        49.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.93        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       10.98        11.01        15.02        12.99        12.00        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.97        30.05        12.95        13.02        10.06         5.29 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.33       129.27        24.13        51.48        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46        11.97         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.25        55.76        47.08        26.43 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.02              0.39 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           126.41            129.27 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            15.35             10.78 
[1] "1.0 - 126.4 (15.3)" "0.4 - 129.3 (10.8)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5P LOSS MUTATED         3        2         6         0         0         2
  5P LOSS WILD-TYPE      27        6        32         2         2         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5P LOSS MUTATED            2          2          3        3         2
  5P LOSS WILD-TYPE          7         21         11       14         7
D49V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    1  3 19  2
  5P LOSS WILD-TYPE  8 26 90 12
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               1                 8
  T2               3                26
  T3              19                90
  T4               2                12
                   vv
clus                N0 N1 N2
  5P LOSS MUTATED   11  8  6
  5P LOSS WILD-TYPE 72 37 26
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              11                72
  N1               8                37
  N2               6                26
                   vv
clus                 M0  M1 M1A  MX
  5P LOSS MUTATED    19   4   0   2
  5P LOSS WILD-TYPE 104  18   2  11
D49V6, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               19               104
  M1                4                18
  M1A               0                 2
  MX                2                11
D49V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   15 10
  5P LOSS WILD-TYPE 59 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     15   10
  5P LOSS WILD-TYPE   59   78
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              15                59
  MALE                10                78
D49V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    24   1
  5P LOSS WILD-TYPE 119  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     24    1
  5P LOSS WILD-TYPE  119   12
                                clus
vv                               5P LOSS MUTATED 5P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       24               119
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D49V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     2  23
  5P LOSS WILD-TYPE   4 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   23
  5P LOSS WILD-TYPE    4  133
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                2                 4
  YES              23               133
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    17   1   2   0
  5P LOSS WILD-TYPE 104   1  10   3
D49V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              17               104
  R1               1                 1
  R2               2                10
  RX               0                 3
D49V11, continuous

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   22  6
  5Q LOSS WILD-TYPE 95  7
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28               102 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                 7 
$`5Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6672 
       24.13        17.23        10.62        25.02        15.35        10.39 
TCGA-AG-3731 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00Y TCGA-AG-A01W 
        1.02         1.02         1.02         1.02        23.01        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 
       63.98         1.94        38.93        10.19         6.02        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD 
       15.02        36.00         6.97        13.02       126.41        57.24 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6881 TCGA-F5-6702 
       51.48        20.55        16.37         2.17 

$`5Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       17.95        13.55        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        8.45        11.67        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        0.99         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.94        17.03        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        12.00        10.98        51.98        49.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        0.72         4.60         1.81         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.70        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        12.99        12.00        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        5.29        41.33       129.27        24.13        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.61        17.46        11.97         8.45         3.39         0.85 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.02              0.39 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           126.41            129.27 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           15.185            10.585 
[1] "1.0 - 126.4 (15.2)" "0.4 - 129.3 (10.6)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5Q LOSS MUTATED         5        3        12         0         0         1
  5Q LOSS WILD-TYPE      25        5        26         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5Q LOSS MUTATED            2          4          4        4         4
  5Q LOSS WILD-TYPE          7         19         10       13         5
D50V3, multiclass
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    1  6 29  3
  5Q LOSS WILD-TYPE  8 23 80 11
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               1                 8
  T2               6                23
  T3              29                80
  T4               3                11
                   vv
clus                N0 N1 N2
  5Q LOSS MUTATED   20 11  8
  5Q LOSS WILD-TYPE 63 34 24
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              20                63
  N1              11                34
  N2               8                24
                   vv
clus                M0 M1 M1A MX
  5Q LOSS MUTATED   28  6   1  3
  5Q LOSS WILD-TYPE 95 16   1 10
D50V6, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               28                95
  M1                6                16
  M1A               1                 1
  MX                3                10
D50V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   20 19
  5Q LOSS WILD-TYPE 54 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     20   19
  5Q LOSS WILD-TYPE   54   69
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              20                54
  MALE                19                69
D50V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    37   1
  5Q LOSS WILD-TYPE 106  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     37    1
  5Q LOSS WILD-TYPE  106   12
                                clus
vv                               5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       37               106
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D50V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5  34
  5Q LOSS WILD-TYPE   1 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5   34
  5Q LOSS WILD-TYPE    1  122
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                5                 1
  YES              34               122
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED   27  1  3  0
  5Q LOSS WILD-TYPE 94  1  9  3
D50V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              27                94
  R1               1                 1
  R2               3                 9
  RX               0                 3
D50V11, continuous

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     7   2
  6P LOSS WILD-TYPE 110  11
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9               121 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                11 
$`6P LOSS MUTATED`
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-A008 TCGA-AG-A011 TCGA-DC-6682 
       17.23        13.55        12.72        13.91        17.03        13.02 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6883 
        5.29        24.13        11.51 

$`6P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        10.62        19.10        25.02        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       14.50         8.45        15.35        11.67        10.39        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
        1.02         1.02         1.02         1.02         0.99        20.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.94        23.01        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        12.00        70.03        63.98        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.94         1.94        38.93        61.94        40.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.01         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.70        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        14.01        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
        6.97        30.05        12.95        10.06       126.41        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.58         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       17.69        16.34        16.31        16.37         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.61        17.46        11.97         8.45         3.39         0.85 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        2.17         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76         0.46        18.25        55.76        47.08 
TCGA-G5-6641 
       26.43 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             5.29              0.39 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            24.13            129.27 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            13.55             10.62 
[1] "5.3 - 24.1 (13.6)"  "0.4 - 129.3 (10.6)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "6.7"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6P LOSS MUTATED         1        1         7         0         1         0
  6P LOSS WILD-TYPE      29        7        31         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6P LOSS MUTATED            0          0          2        2         0
  6P LOSS WILD-TYPE          9         23         12       15         9
D51V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    0  1 13  0
  6P LOSS WILD-TYPE  9 28 96 14
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               0                 9
  T2               1                28
  T3              13                96
  T4               0                14
                   vv
clus                N0 N1 N2
  6P LOSS MUTATED   10  0  4
  6P LOSS WILD-TYPE 73 45 28
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              10                73
  N1               0                45
  N2               4                28
                   vv
clus                 M0  M1 M1A  MX
  6P LOSS MUTATED    12   2   0   0
  6P LOSS WILD-TYPE 111  20   2  13
D51V6, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               12               111
  M1                2                20
  M1A               0                 2
  MX                0                13
D51V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    6  8
  6P LOSS WILD-TYPE 68 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      6    8
  6P LOSS WILD-TYPE   68   80
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               6                68
  MALE                 8                80
D51V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    10   3
  6P LOSS WILD-TYPE 133  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     10    3
  6P LOSS WILD-TYPE  133   10
                                clus
vv                               6P LOSS MUTATED 6P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       10               133
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
D51V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  13
  6P LOSS WILD-TYPE   5 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   13
  6P LOSS WILD-TYPE    5  143
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                1                 5
  YES              13               143
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    11   0   1   1
  6P LOSS WILD-TYPE 110   2  11   2
D51V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              11               110
  R1               0                 2
  R2               1                11
  RX               1                 2
D51V11, continuous

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    12   2
  6Q LOSS WILD-TYPE 105  11
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14               116 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                11 
$`6Q LOSS MUTATED`
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3587 
       17.23        13.55        19.10        12.72        12.00         1.02 
TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6883 
       13.91        17.03         0.49        13.02         5.29        11.51 
TCGA-G5-6233 TCGA-G5-6641 
       18.25        26.43 

$`6Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       24.13        17.95        10.62        25.02        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 
        8.45        15.35        11.67        10.39         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        2.01         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         0.99        20.94         6.02        25.94        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        63.98        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
       38.93        61.94        40.96        38.01         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        36.00         6.97        30.05        12.95        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.41        41.33        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.58         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.37         8.61        10.78        13.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         3.39         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.08         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.49              0.39 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            26.43            129.27 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           13.285            10.505 
[1] "0.5 - 26.4 (13.3)"  "0.4 - 129.3 (10.5)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
[1] "hr=" "4.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6Q LOSS MUTATED         3        2         8         0         2         0
  6Q LOSS WILD-TYPE      27        6        30         2         0         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6Q LOSS MUTATED            1          0          3        2         0
  6Q LOSS WILD-TYPE          8         23         11       15         9
D52V3, multiclass
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    1  3 18  0
  6Q LOSS WILD-TYPE  8 26 91 14
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               1                 8
  T2               3                26
  T3              18                91
  T4               0                14
                   vv
clus                N0 N1 N2
  6Q LOSS MUTATED   14  2  6
  6Q LOSS WILD-TYPE 69 43 26
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              14                69
  N1               2                43
  N2               6                26
                   vv
clus                 M0  M1 M1A  MX
  6Q LOSS MUTATED    17   3   0   2
  6Q LOSS WILD-TYPE 106  19   2  11
D52V6, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               17               106
  M1                3                19
  M1A               0                 2
  MX                2                11
D52V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    7 15
  6Q LOSS WILD-TYPE 67 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7   15
  6Q LOSS WILD-TYPE   67   73
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               7                67
  MALE                15                73
D52V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    15   5
  6Q LOSS WILD-TYPE 128   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15    5
  6Q LOSS WILD-TYPE  128    8
                                clus
vv                               6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       15               128
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
D52V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  21
  6Q LOSS WILD-TYPE   5 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   21
  6Q LOSS WILD-TYPE    5  135
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                 5
  YES              21               135
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    18   0   1   1
  6Q LOSS WILD-TYPE 103   2  11   2
D52V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              18               103
  R1               0                 2
  R2               1                11
  RX               1                 2
D52V11, continuous

Clustering(53) Variable = 8P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   51  8
  8P LOSS WILD-TYPE 66  5
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               59                71 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                 5 
$`8P LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        10.62        13.55        19.10        25.02 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 
       10.39        15.35        10.39         1.02         1.02         1.02 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3893 
        0.99         7.96         0.95         0.99         1.02         0.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02         1.02         1.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       15.91         1.02        12.00        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 
       38.93        40.96         1.45        10.19         4.70        13.97 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       60.00        10.98        11.01        14.01        36.00         6.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5831 
       10.06         5.29       126.41       129.27        51.48         2.40 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       15.85        16.34        10.78        11.97         8.45         0.85 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        2.17         0.69         0.46        18.25        26.43 

$`8P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3575 
       24.13        12.72        14.50         8.45        11.67        12.00 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3887 
        1.02         2.01         0.99         1.02         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
        1.02         0.99         1.02         1.02         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W 
       13.91         6.02        13.02         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       63.98        49.94        61.94        38.01         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        9.37         7.99        15.02        12.99        12.00        15.02 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       30.05        12.95        13.02        41.33        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.58         0.49        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        17.69        16.31        16.37         8.61        11.51 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       13.61        17.46         3.39         0.39         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.08         0.76        55.76        47.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.46              0.39 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           129.27             70.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            10.78             12.00 
[1] "0.5 - 129.3 (10.8)" "0.4 - 70.0 (12.0)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
[1] "hr=" "2"  
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8P LOSS MUTATED        14        2        17         0         1         3
  8P LOSS WILD-TYPE      16        6        21         2         1         2
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8P LOSS MUTATED            4         11          8        9         3
  8P LOSS WILD-TYPE          5         12          6        8         6
D53V3, multiclass
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    3 14 50  7
  8P LOSS WILD-TYPE  6 15 59  7
D53V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                 6
  T2              14                15
  T3              50                59
  T4               7                 7
                   vv
clus                N0 N1 N2
  8P LOSS MUTATED   34 23 17
  8P LOSS WILD-TYPE 49 22 15
D53V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              34                49
  N1              23                22
  N2              17                15
                   vv
clus                M0 M1 M1A MX
  8P LOSS MUTATED   55 11   0  7
  8P LOSS WILD-TYPE 68 11   2  6
D53V6, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               55                68
  M1               11                11
  M1A               0                 2
  MX                7                 6
D53V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   32 42
  8P LOSS WILD-TYPE 42 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     32   42
  8P LOSS WILD-TYPE   42   46
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              32                42
  MALE                42                46
D53V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   66  5
  8P LOSS WILD-TYPE 77  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     66    5
  8P LOSS WILD-TYPE   77    8
                                clus
vv                               8P LOSS MUTATED 8P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       66                77
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
D53V9, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4 70
  8P LOSS WILD-TYPE  2 86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4   70
  8P LOSS WILD-TYPE    2   86
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4                 2
  YES              70                86
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   55  1  6  2
  8P LOSS WILD-TYPE 66  1  6  1
D53V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              55                66
  R1               1                 1
  R2               6                 6
  RX               2                 1
D53V11, continuous

Clustering(54) Variable = 8Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     8   1
  8Q LOSS WILD-TYPE 109  12
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                9               121 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                12 
$`8Q LOSS MUTATED`
TCGA-AG-3605 TCGA-AG-3883 TCGA-AG-4001 TCGA-AG-A01L TCGA-AG-A02X TCGA-DC-6157 
        0.99         1.02         1.02        12.00        40.96        36.00 
TCGA-DY-A1DG TCGA-EI-6511 TCGA-F5-6813 
       51.48        15.85         0.69 

$`8Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         1.02         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         0.99         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
        1.02         1.02         1.02         1.02         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.91         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       13.02         1.02         1.02        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.01         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.70        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       15.02        12.99        12.00        14.01        15.02         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.02        10.06         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       41.33        57.24       129.27        24.13        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.37         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       10.78        13.61        17.46        11.97         8.45         3.39 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
        0.85         2.17         0.39         1.02         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76         0.46        18.25        55.76        47.08 
TCGA-G5-6641 
       26.43 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.69              0.39 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            51.48            129.27 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            12.00             10.98 
[1] "0.7 - 51.5 (12.0)"  "0.4 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8Q LOSS MUTATED         4        0         2         0         0         0
  8Q LOSS WILD-TYPE      26        8        36         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8Q LOSS MUTATED            0          2          1        1         1
  8Q LOSS WILD-TYPE          9         21         13       16         8
D54V3, multiclass
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED     0   4   6   1
  8Q LOSS WILD-TYPE   9  25 103  13
D54V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                 9
  T2               4                25
  T3               6               103
  T4               1                13
                   vv
clus                N0 N1 N2
  8Q LOSS MUTATED    6  4  1
  8Q LOSS WILD-TYPE 77 41 31
D54V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               6                77
  N1               4                41
  N2               1                31
                   vv
clus                 M0  M1 M1A  MX
  8Q LOSS MUTATED     9   2   0   0
  8Q LOSS WILD-TYPE 114  20   2  13
D54V6, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0                9               114
  M1                2                20
  M1A               0                 2
  MX                0                13
D54V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  9
  8Q LOSS WILD-TYPE 72 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    9
  8Q LOSS WILD-TYPE   72   79
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               2                72
  MALE                 9                79
D54V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    11   0
  8Q LOSS WILD-TYPE 132  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11    0
  8Q LOSS WILD-TYPE  132   13
                                clus
vv                               8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       11               132
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
D54V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  11
  8Q LOSS WILD-TYPE   6 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   11
  8Q LOSS WILD-TYPE    6  145
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 6
  YES              11               145
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED     9   0   1   0
  8Q LOSS WILD-TYPE 112   2  11   3
D54V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               9               112
  R1               0                 2
  R2               1                11
  RX               0                 3
D54V11, continuous

Clustering(55) Variable = 9P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    14   4
  9P LOSS WILD-TYPE 103   9
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18               112 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                 9 
$`9P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AG-3583 TCGA-AG-3731 TCGA-AG-A014 TCGA-AG-A01L 
       24.13        13.55         2.01         1.02        15.91        12.00 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 
       12.00         1.94        38.93         6.02         4.70        13.97 
TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6514 
       11.01         6.97        30.05        51.48         0.49        16.31 

$`9P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        10.62        19.10        12.72        25.02 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.35        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
       12.00         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99         7.96         0.95         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.94        23.01        17.03        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81        10.19         6.02         6.94 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
        9.37        60.00         7.99        10.98        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       12.00        14.01        15.02        36.00        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.58         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.37 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         3.39         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.08         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        55.76        47.08        26.43 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.49              0.39 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            51.48            129.27 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            12.00             10.88 
[1] "0.5 - 51.5 (12.0)"  "0.4 - 129.3 (10.9)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "4"  
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9P LOSS MUTATED         6        1         3         1         0         0
  9P LOSS WILD-TYPE      24        7        35         1         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9P LOSS MUTATED            1          1          2        6         1
  9P LOSS WILD-TYPE          8         22         12       11         8
D55V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    0  8 12  2
  9P LOSS WILD-TYPE  9 21 97 12
D55V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               0                 9
  T2               8                21
  T3              12                97
  T4               2                12
                   vv
clus                N0 N1 N2
  9P LOSS MUTATED   12  6  4
  9P LOSS WILD-TYPE 71 39 28
D55V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              12                71
  N1               6                39
  N2               4                28
                   vv
clus                 M0  M1 M1A  MX
  9P LOSS MUTATED    15   7   0   0
  9P LOSS WILD-TYPE 108  15   2  13
D55V6, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               15               108
  M1                7                15
  M1A               0                 2
  MX                0                13
D55V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    8 14
  9P LOSS WILD-TYPE 66 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8   14
  9P LOSS WILD-TYPE   66   74
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               8                66
  MALE                14                74
D55V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    20   1
  9P LOSS WILD-TYPE 123  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     20    1
  9P LOSS WILD-TYPE  123   12
                                clus
vv                               9P LOSS MUTATED 9P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       20               123
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D55V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     1  21
  9P LOSS WILD-TYPE   5 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   21
  9P LOSS WILD-TYPE    5  135
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                1                 5
  YES              21               135
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    12   1   5   0
  9P LOSS WILD-TYPE 109   1   7   3
D55V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              12               109
  R1               1                 1
  R2               5                 7
  RX               0                 3
D55V11, continuous

Clustering(56) Variable = 9Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    15   3
  9Q LOSS WILD-TYPE 102  10
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               18               112 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                10 
$`9Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AG-3583 TCGA-AG-3731 TCGA-AG-A014 TCGA-AG-A01L 
       24.13        13.55         2.01         1.02        15.91        12.00 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 
       12.00         1.94        38.93         6.02         4.70        13.97 
TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-EF-5830 TCGA-EI-6514 TCGA-F5-6702 
       11.01         6.97        30.05         0.49        16.31         2.17 

$`9Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        10.62        19.10        12.72        25.02 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.35        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
       12.00         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99         7.96         0.95         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.94        23.01        17.03        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81        10.19         6.02         6.94 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
        9.37        60.00         7.99        10.98        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       12.00        14.01        15.02        36.00        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.58         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.37         8.61        11.51        10.78        13.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45         3.39         0.85         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.08         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        55.76        47.08        26.43 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.49              0.39 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            38.93            129.27 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           11.505            10.980 
[1] "0.5 - 38.9 (11.5)"  "0.4 - 129.3 (11.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "5.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9Q LOSS MUTATED         6        1         3         1         0         0
  9Q LOSS WILD-TYPE      24        7        35         1         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9Q LOSS MUTATED            1          2          1        5         1
  9Q LOSS WILD-TYPE          8         21         13       12         8
D56V3, multiclass
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED    0  8 10  3
  9Q LOSS WILD-TYPE  9 21 99 11
D56V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               0                 9
  T2               8                21
  T3              10                99
  T4               3                11
                   vv
clus                N0 N1 N2
  9Q LOSS MUTATED   12  7  2
  9Q LOSS WILD-TYPE 71 38 30
D56V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              12                71
  N1               7                38
  N2               2                30
                   vv
clus                 M0  M1 M1A  MX
  9Q LOSS MUTATED    15   6   0   0
  9Q LOSS WILD-TYPE 108  16   2  13
D56V6, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               15               108
  M1                6                16
  M1A               0                 2
  MX                0                13
D56V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    7 14
  9Q LOSS WILD-TYPE 67 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7   14
  9Q LOSS WILD-TYPE   67   74
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               7                67
  MALE                14                74
D56V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    19   1
  9Q LOSS WILD-TYPE 124  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     19    1
  9Q LOSS WILD-TYPE  124   12
                                clus
vv                               9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       19               124
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
D56V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  20
  9Q LOSS WILD-TYPE   5 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   20
  9Q LOSS WILD-TYPE    5  136
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 5
  YES              20               136
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    12   1   5   0
  9Q LOSS WILD-TYPE 109   1   7   3
D56V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              12               109
  R1               1                 1
  R2               5                 7
  RX               0                 3
D56V11, continuous

Clustering(57) Variable = 10P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   29  0
  10P LOSS WILD-TYPE 88 13
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                29                101 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                 13 
$`10P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3587 
       24.13        13.55        12.72        15.35        10.39         1.02 
TCGA-AG-3887 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X 
        0.92        13.91        25.94        12.00        10.98        40.96 
TCGA-AH-6544 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 
        0.49         4.70        14.01        15.02        36.00        13.02 
TCGA-DC-6683 TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 
       10.06       129.27         0.49        17.00        16.34        16.31 
TCGA-EI-6881 TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
       16.37         8.45         2.17         0.46        26.43 

$`10P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        10.62        19.10        25.02        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       14.50         8.45        11.67        12.00         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        2.01         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 
        1.02         0.99         0.99         1.02         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
        0.99        20.94         6.02        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       13.02         1.02         1.02        12.00        70.03        63.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.94         1.94        38.93        61.94        38.01 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.02         6.94         9.37        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        6.97        30.05        12.95         5.29       126.41        41.33 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24        24.13        51.48        32.58         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 
       19.96        20.91        18.28        15.85        17.69         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
       11.51        10.78        13.61        17.46        11.97         3.39 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        0.85         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76        18.25        55.76        47.08 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.46               0.39 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            129.27             126.41 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             13.55              10.39 
[1] "0.5 - 129.3 (13.6)" "0.4 - 126.4 (10.4)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "10P LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "10P LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "10P LOSS MUTATED" 
[1] "hr="     "2.6e+08"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10P LOSS MUTATED         5        0         9         1         0         1
  10P LOSS WILD-TYPE      25        8        29         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10P LOSS MUTATED            3          5          3        1         3
  10P LOSS WILD-TYPE          6         18         11       16         6
D57V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    1  6 21  4
  10P LOSS WILD-TYPE  8 23 88 10
D57V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                  8
  T2                6                 23
  T3               21                 88
  T4                4                 10
                    vv
clus                 N0 N1 N2
  10P LOSS MUTATED   15 11  6
  10P LOSS WILD-TYPE 68 34 26
D57V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               15                 68
  N1               11                 34
  N2                6                 26
                    vv
clus                 M0 M1 M1A MX
  10P LOSS MUTATED   26  2   1  3
  10P LOSS WILD-TYPE 97 20   1 10
D57V6, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                26                 97
  M1                 2                 20
  M1A                1                  1
  MX                 3                 10
D57V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   13 19
  10P LOSS WILD-TYPE 61 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     13   19
  10P LOSS WILD-TYPE   61   69
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               13                 61
  MALE                 19                 69
D57V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    25   6
  10P LOSS WILD-TYPE 118   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     25    6
  10P LOSS WILD-TYPE  118    7
                                clus
vv                               10P LOSS MUTATED 10P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        25                118
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
D57V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4  28
  10P LOSS WILD-TYPE   2 128
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4   28
  10P LOSS WILD-TYPE    2  128
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 4                  2
  YES               28                128
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED   27  0  0  0
  10P LOSS WILD-TYPE 94  2 12  3
D57V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               27                 94
  R1                0                  2
  R2                0                 12
  RX                0                  3
D57V11, continuous

Clustering(58) Variable = 10Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   29  1
  10Q LOSS WILD-TYPE 88 12
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                30                100 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                 12 
$`10Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3587 
       24.13        13.55        12.72        15.35        10.39         1.02 
TCGA-AG-3887 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A020 
        0.92        13.91        25.94        17.03        12.00        10.98 
TCGA-AG-A02X TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       40.96         4.70        14.01        36.00        13.02        10.06 
TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
      129.27         0.49        17.00        16.34        16.31        16.37 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       11.97         2.17         0.66         0.46        47.08        26.43 

$`10Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        10.62        19.10        25.02        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       14.50         8.45        11.67        12.00         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        2.01         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 
        1.02         0.99         0.99         1.02         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.94         6.02        23.01        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        1.02         1.02        12.00        70.03        63.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.94         1.94        38.93        61.94        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.02         6.94         9.37        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       15.02         6.97        30.05        12.95         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       41.33        57.24        24.13        51.48        32.58         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.61        17.46         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
        3.39         0.85         0.39         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        1.08         0.76        18.25        55.76 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.46               0.39 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            129.27             126.41 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             13.73               9.78 
[1] "0.5 - 129.3 (13.7)" "0.4 - 126.4 (9.8)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G5-6641 
  "10Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G5-6641 
  "10Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-G5-6641 
  "10Q LOSS MUTATED" 
[1] "hr=" "3.2"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10Q LOSS MUTATED         5        0        13         1         0         1
  10Q LOSS WILD-TYPE      25        8        25         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10Q LOSS MUTATED            3          6          4        2         1
  10Q LOSS WILD-TYPE          6         17         10       15         8
D58V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    1  6 27  2
  10Q LOSS WILD-TYPE  8 23 82 12
D58V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                1                  8
  T2                6                 23
  T3               27                 82
  T4                2                 12
                    vv
clus                 N0 N1 N2
  10Q LOSS MUTATED   19 11  6
  10Q LOSS WILD-TYPE 64 34 26
D58V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               19                 64
  N1               11                 34
  N2                6                 26
                    vv
clus                 M0 M1 M1A MX
  10Q LOSS MUTATED   31  2   0  3
  10Q LOSS WILD-TYPE 92 20   2 10
D58V6, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                31                 92
  M1                 2                 20
  M1A                0                  2
  MX                 3                 10
D58V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   14 23
  10Q LOSS WILD-TYPE 60 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     14   23
  10Q LOSS WILD-TYPE   60   65
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               14                 60
  MALE                 23                 65
D58V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    30   6
  10Q LOSS WILD-TYPE 113   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     30    6
  10Q LOSS WILD-TYPE  113    7
                                clus
vv                               10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        30                113
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
D58V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4  33
  10Q LOSS WILD-TYPE   2 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4   33
  10Q LOSS WILD-TYPE    2  123
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 4                  2
  YES               33                123
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED   32  0  0  0
  10Q LOSS WILD-TYPE 89  2 12  3
D58V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               32                 89
  R1                0                  2
  R2                0                 12
  RX                0                  3
D58V11, continuous

Clustering(59) Variable = 11P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    17   1
  11P LOSS WILD-TYPE 100  12
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                112 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 12 
$`11P LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-A008 
       10.62        14.50        15.35        10.39         1.02        13.91 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 
       12.00        10.98        40.96         0.49         0.69        14.01 
TCGA-DC-6156 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 TCGA-F5-6813 
       15.02         5.29        24.13        17.00        16.37         0.69 

$`11P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3582 
       25.02        10.39         8.45        11.67        12.00         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        2.01         1.02         1.02         0.99         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02         0.99        20.94         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        63.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       38.93        61.94        38.01         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.70        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        12.00        36.00         6.97        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.02        10.06       126.41        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.58         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         0.66         0.53         1.08         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        55.76        47.08        26.43 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.49               0.39 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             40.96             129.27 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            12.955             10.880 
[1] "0.5 - 41.0 (13.0)"  "0.4 - 129.3 (10.9)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11P LOSS MUTATED         5        1         3         0         0         1
  11P LOSS WILD-TYPE      25        7        35         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11P LOSS MUTATED            2          3          5        1         2
  11P LOSS WILD-TYPE          7         20          9       16         7
D59V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    1  5 14  4
  11P LOSS WILD-TYPE  8 24 95 10
D59V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                  8
  T2                5                 24
  T3               14                 95
  T4                4                 10
                    vv
clus                 N0 N1 N2
  11P LOSS MUTATED    9  7  8
  11P LOSS WILD-TYPE 74 38 24
D59V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                9                 74
  N1                7                 38
  N2                8                 24
                    vv
clus                  M0  M1 M1A  MX
  11P LOSS MUTATED    19   1   1   3
  11P LOSS WILD-TYPE 104  21   1  10
D59V6, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                19                104
  M1                 1                 21
  M1A                1                  1
  MX                 3                 10
D59V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   11 13
  11P LOSS WILD-TYPE 63 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     11   13
  11P LOSS WILD-TYPE   63   75
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               11                 63
  MALE                 13                 75
D59V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    18   4
  11P LOSS WILD-TYPE 125   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18    4
  11P LOSS WILD-TYPE  125    9
                                clus
vv                               11P LOSS MUTATED 11P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        18                125
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
D59V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  22
  11P LOSS WILD-TYPE   4 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   22
  11P LOSS WILD-TYPE    4  134
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 2                  4
  YES               22                134
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    18   0   0   1
  11P LOSS WILD-TYPE 103   2  12   2
D59V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               18                103
  R1                0                  2
  R2                0                 12
  RX                1                  2
D59V11, continuous

Clustering(60) Variable = 11Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   19  2
  11Q LOSS WILD-TYPE 98 11
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                109 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 11 
$`11Q LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       10.62        13.55        19.10        14.50        15.35        10.39 
TCGA-AG-3581 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A020 TCGA-AH-6544 TCGA-AH-6643 
        1.02        13.91        12.00        10.98         0.49         0.69 
TCGA-BM-6198 TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 
       10.19        13.97        14.01         6.97        30.05         5.29 
TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 
       24.13        17.00        16.37 

$`11Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        12.72        25.02        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        8.45        11.67        12.00         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.94         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       15.91        13.02         1.02         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       63.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       40.96        38.01         1.45         0.72         4.60         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        6.02         6.02         6.94         9.37         4.70        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        36.00        12.95        13.02        10.06       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.33        57.24       129.27        51.48        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.61        17.46        11.97         8.45         3.39         0.85 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        2.17         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76         0.46        18.25        55.76        47.08 
TCGA-G5-6641 
       26.43 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.49               0.39 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             30.05             129.27 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             13.55              10.78 
[1] "0.5 - 30.1 (13.6)"  "0.4 - 129.3 (10.8)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11Q LOSS WILD-TYPE" 
[1] "hr=" "3"  
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11Q LOSS MUTATED         7        1         6         0         0         1
  11Q LOSS WILD-TYPE      23        7        32         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11Q LOSS MUTATED            3          4          4        1         1
  11Q LOSS WILD-TYPE          6         19         10       16         8
D60V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    1  7 19  2
  11Q LOSS WILD-TYPE  8 22 90 12
D60V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                  8
  T2                7                 22
  T3               19                 90
  T4                2                 12
                    vv
clus                 N0 N1 N2
  11Q LOSS MUTATED   14  9  6
  11Q LOSS WILD-TYPE 69 36 26
D60V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               14                 69
  N1                9                 36
  N2                6                 26
                    vv
clus                  M0  M1 M1A  MX
  11Q LOSS MUTATED    23   1   0   4
  11Q LOSS WILD-TYPE 100  21   2   9
D60V6, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                23                100
  M1                 1                 21
  M1A                0                  2
  MX                 4                  9
D60V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   13 16
  11Q LOSS WILD-TYPE 61 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     13   16
  11Q LOSS WILD-TYPE   61   72
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               13                 61
  MALE                 16                 72
D60V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    20   5
  11Q LOSS WILD-TYPE 123   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     20    5
  11Q LOSS WILD-TYPE  123    8
                                clus
vv                               11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        20                123
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
D60V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  26
  11Q LOSS WILD-TYPE   3 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   26
  11Q LOSS WILD-TYPE    3  130
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 3                  3
  YES               26                130
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED    21   0   0   1
  11Q LOSS WILD-TYPE 100   2  12   2
D60V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               21                100
  R1                0                  2
  R2                0                 12
  RX                1                  2
D60V11, continuous

Clustering(61) Variable = 12P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    12   4
  12P LOSS WILD-TYPE 105   9
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                16                114 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                  9 
$`12P LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-A00Y TCGA-AG-A01W 
       10.62        10.39        14.50        15.35        23.01        70.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 TCGA-EI-6509 
       14.01         6.97        24.13        51.48        20.91        17.00 
TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       16.31        16.37         2.17         0.66 

$`12P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 
       25.02         8.45        11.67        10.39        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        7.96         0.95         1.02         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.94        17.03        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        12.00        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.02         6.02         6.94         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       12.99        12.00        15.02        36.00        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.02        10.06         5.29       126.41        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      129.27        32.58         0.49         2.40        20.55        19.96 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        17.69        16.34         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       10.78        13.61        17.46        11.97         8.45         3.39 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.85         0.39         1.02         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.66               0.39 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             70.03             129.27 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            15.830             10.585 
[1] "0.7 - 70.0 (15.8)"  "0.4 - 129.3 (10.6)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "12P LOSS MUTATED"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12P LOSS WILD-TYPE" 
[1] "hr=" "2.5"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12P LOSS MUTATED         2        1         7         0         0         0
  12P LOSS WILD-TYPE      28        7        31         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12P LOSS MUTATED            2          3          3        1         3
  12P LOSS WILD-TYPE          7         20         11       16         6
D61V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    1  2 19  1
  12P LOSS WILD-TYPE  8 27 90 13
D61V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                  8
  T2                2                 27
  T3               19                 90
  T4                1                 13
                    vv
clus                 N0 N1 N2
  12P LOSS MUTATED   10  8  5
  12P LOSS WILD-TYPE 73 37 27
D61V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               10                 73
  N1                8                 37
  N2                5                 27
                    vv
clus                  M0  M1 M1A  MX
  12P LOSS MUTATED    17   4   0   2
  12P LOSS WILD-TYPE 106  18   2  11
D61V6, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                17                106
  M1                 4                 18
  M1A                0                  2
  MX                 2                 11
D61V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   12 11
  12P LOSS WILD-TYPE 62 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12   11
  12P LOSS WILD-TYPE   62   77
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               12                 62
  MALE                 11                 77
D61V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    22   0
  12P LOSS WILD-TYPE 121  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     22    0
  12P LOSS WILD-TYPE  121   13
                                clus
vv                               12P LOSS MUTATED 12P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        22                121
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D61V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  22
  12P LOSS WILD-TYPE   5 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   22
  12P LOSS WILD-TYPE    5  134
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 1                  5
  YES               22                134
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    19   0   1   0
  12P LOSS WILD-TYPE 102   2  11   3
D61V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               19                102
  R1                0                  2
  R2                1                 11
  RX                0                  3
D61V11, continuous

Clustering(62) Variable = 12Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    13   3
  12Q LOSS WILD-TYPE 104  10
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                16                114 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 10 
$`12Q LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-4001 TCGA-AG-A00Y TCGA-AG-A014 
       10.62        14.50        15.35         1.02        23.01        15.91 
TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6509 
        0.49        14.01         6.97        24.13        51.48        17.00 
TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       16.31        16.37         2.17         0.66 

$`12Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       25.02        10.39         8.45        11.67        10.39        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        25.94        17.03        13.02         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.02         6.02         6.94         9.37         4.70        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.00         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.00        15.02        36.00        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.41        41.33        57.24       129.27 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.58         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        17.69        16.34         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       10.78        13.61        17.46        11.97         8.45         3.39 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.85         0.39         1.02         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.49               0.39 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             51.48             129.27 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            14.925             10.880 
[1] "0.5 - 51.5 (14.9)"  "0.4 - 129.3 (10.9)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12Q LOSS WILD-TYPE" 
[1] "hr=" "3.5"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12Q LOSS MUTATED         3        0         7         0         0         0
  12Q LOSS WILD-TYPE      27        8        31         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12Q LOSS MUTATED            2          2          2        1         3
  12Q LOSS WILD-TYPE          7         21         12       16         6
D62V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    1  3 16  1
  12Q LOSS WILD-TYPE  8 26 93 13
D62V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                  8
  T2                3                 26
  T3               16                 93
  T4                1                 13
                    vv
clus                 N0 N1 N2
  12Q LOSS MUTATED   10  7  4
  12Q LOSS WILD-TYPE 73 38 28
D62V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               10                 73
  N1                7                 38
  N2                4                 28
                    vv
clus                  M0  M1 M1A  MX
  12Q LOSS MUTATED    15   4   0   2
  12Q LOSS WILD-TYPE 108  18   2  11
D62V6, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                15                108
  M1                 4                 18
  M1A                0                  2
  MX                 2                 11
D62V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    9 12
  12Q LOSS WILD-TYPE 65 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      9   12
  12Q LOSS WILD-TYPE   65   76
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                9                 65
  MALE                 12                 76
D62V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    20   0
  12Q LOSS WILD-TYPE 123  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     20    0
  12Q LOSS WILD-TYPE  123   13
                                clus
vv                               12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        20                123
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
D62V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  20
  12Q LOSS WILD-TYPE   5 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   20
  12Q LOSS WILD-TYPE    5  136
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                  5
  YES               20                136
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    16   0   1   0
  12Q LOSS WILD-TYPE 105   2  11   3
D62V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               16                105
  R1                0                  2
  R2                1                 11
  RX                0                  3
D62V11, continuous

Clustering(63) Variable = 13Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     4   0
  13Q LOSS WILD-TYPE 113  13
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                126 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                 13 
$`13Q LOSS MUTATED`
TCGA-AG-A00Y TCGA-AG-A020 TCGA-DC-6156 TCGA-DY-A0XA 
       23.01        10.98        15.02       126.41 

$`13Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        63.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.93        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.94         9.37         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       14.01        36.00         6.97        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06         5.29        41.33        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.58         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.37         8.61        11.51        10.78        13.61 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46        11.97         8.45         3.39         0.85         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             10.98               0.39 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            126.41             129.27 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            19.015             10.880 
[1] "11.0 - 126.4 (19.0)" "0.4 - 129.3 (10.9)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"13Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"13Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"13Q LOSS WILD-TYPE" 
[1] "hr="     "7.6e+07"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  13Q LOSS MUTATED         0        0         4         0         0         1
  13Q LOSS WILD-TYPE      30        8        34         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  13Q LOSS MUTATED            0          0          1        1         1
  13Q LOSS WILD-TYPE          9         23         13       16         8
D63V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED     0   0   7   1
  13Q LOSS WILD-TYPE   9  29 102  13
D63V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                0                  9
  T2                0                 29
  T3                7                102
  T4                1                 13
                    vv
clus                 N0 N1 N2
  13Q LOSS MUTATED    4  1  3
  13Q LOSS WILD-TYPE 79 44 29
D63V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                4                 79
  N1                1                 44
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  13Q LOSS MUTATED     6   1   1   0
  13Q LOSS WILD-TYPE 117  21   1  13
D63V6, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                 6                117
  M1                 1                 21
  M1A                1                  1
  MX                 0                 13
D63V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    4  4
  13Q LOSS WILD-TYPE 70 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    4
  13Q LOSS WILD-TYPE   70   84
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 70
  MALE                  4                 84
D63V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     6   2
  13Q LOSS WILD-TYPE 137  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6    2
  13Q LOSS WILD-TYPE  137   11
                                clus
vv                               13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                137
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
D63V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0   8
  13Q LOSS WILD-TYPE   6 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0    8
  13Q LOSS WILD-TYPE    6  148
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 0                  6
  YES                8                148
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED     6   0   1   0
  13Q LOSS WILD-TYPE 115   2  11   3
D63V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                6                115
  R1                0                  2
  R2                1                 11
  RX                0                  3
D63V11, continuous

Clustering(64) Variable = 14Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   45  6
  14Q LOSS WILD-TYPE 72  7
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                51                 79 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                  7 
$`14Q LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-6672 TCGA-AG-3582 
       17.95        17.23        13.55        25.02        10.39         1.02 
TCGA-AG-3587 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-4001 
        1.02         0.95         0.99         1.02         0.99         1.02 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G 
        1.02         6.02        25.94        23.01         1.94        38.93 
TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 
       38.01         0.49        10.19         6.02         6.02         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
        4.70        13.97         7.99        11.01        12.99        14.01 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG 
       36.00         6.97        13.02        10.06       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 
       20.55        17.00        16.34        16.31        16.37        10.78 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 
       11.97         0.85         0.39         1.02         0.66         0.76 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.25        55.76        26.43 

$`14Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       24.13        10.62        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 
        8.45        15.35        11.67        12.00         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 
        1.02         0.99         0.99         7.96         1.02         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 
        0.92         1.02         0.99         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.94        13.91        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        1.02         1.02        12.00        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       10.98        51.98        49.94        61.94        40.96         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         4.60         1.81         6.94        60.00 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
       10.98        15.02        12.00        15.02        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.41        41.33        57.24        24.13        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       17.69         8.61        11.51        13.61        17.46         8.45 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        3.39         2.17         0.69         0.53         1.08         0.46 
TCGA-G5-6572 
       47.08 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.39               0.46 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            129.27             126.41 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             10.78              11.51 
[1] "0.4 - 129.3 (10.8)" "0.5 - 126.4 (11.5)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "14Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "14Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "14Q LOSS MUTATED" 
[1] "hr=" "1.9"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  14Q LOSS MUTATED         9        1        21         0         1         1
  14Q LOSS WILD-TYPE      21        7        17         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  14Q LOSS MUTATED            5         11          5        7         2
  14Q LOSS WILD-TYPE          4         12          9       10         7
D64V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    3  9 48  4
  14Q LOSS WILD-TYPE  6 20 61 10
D64V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                3                  6
  T2                9                 20
  T3               48                 61
  T4                4                 10
                    vv
clus                 N0 N1 N2
  14Q LOSS MUTATED   31 23 10
  14Q LOSS WILD-TYPE 52 22 22
D64V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               31                 52
  N1               23                 22
  N2               10                 22
                    vv
clus                 M0 M1 M1A MX
  14Q LOSS MUTATED   49  9   0  5
  14Q LOSS WILD-TYPE 74 13   2  8
D64V6, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                49                 74
  M1                 9                 13
  M1A                0                  2
  MX                 5                  8
D64V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   25 39
  14Q LOSS WILD-TYPE 49 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     25   39
  14Q LOSS WILD-TYPE   49   49
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               25                 49
  MALE                 39                 49
D64V8, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   61  1
  14Q LOSS WILD-TYPE 82 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     61    1
  14Q LOSS WILD-TYPE   82   12
                                clus
vv                               14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        61                 82
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D64V9, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    3 61
  14Q LOSS WILD-TYPE  3 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3   61
  14Q LOSS WILD-TYPE    3   95
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 3                  3
  YES               61                 95
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED   46  2  3  1
  14Q LOSS WILD-TYPE 75  0  9  2
D64V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               46                 75
  R1                2                  0
  R2                3                  9
  RX                1                  2
D64V11, continuous

Clustering(65) Variable = 15Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   47  6
  15Q LOSS WILD-TYPE 70  7
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                53                 77 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                  7 
$`15Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 
       24.13        10.62        13.55        25.02        14.50        10.39 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-3999 
        1.02         2.01         1.02         0.99         0.99         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
        1.02        13.91        25.94        23.01        17.03         1.02 
TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       12.00         1.94        38.93        40.96        38.01         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 
        0.69        10.19         6.02         9.37         7.99        10.98 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.99        14.01        36.00        13.02        41.33        57.24 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 
       24.13         0.49         2.40        15.85        16.31        16.37 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       11.51        10.78        13.61        11.97         0.85         2.17 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        1.02         0.66         0.69        18.25        26.43 

$`15Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       17.95        17.23        19.10        12.72        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3599 
       15.35        11.67        12.00         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 
        0.99         7.96         0.95         1.02         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 
        0.92         1.02         0.99         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        0.99        20.94         6.02        15.91        13.02         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       61.94         1.45         0.72         4.60         1.81         6.02 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 
        6.94         4.70        13.97        60.00        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       12.00        15.02         6.97        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
        5.29       126.41       129.27        51.48        32.58        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 
        8.61        17.46         8.45         3.39         0.39         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76         0.46        55.76        47.08 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.49               0.39 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             57.24             129.27 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             11.51              10.98 
[1] "0.5 - 57.2 (11.5)"  "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "15Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "15Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "15Q LOSS MUTATED" 
[1] "hr=" "2.4"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  15Q LOSS MUTATED         9        1        20         1         2         2
  15Q LOSS WILD-TYPE      21        7        18         1         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  15Q LOSS MUTATED            4         12          7        9         2
  15Q LOSS WILD-TYPE          5         11          7        8         7
D65V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    4  8 53  5
  15Q LOSS WILD-TYPE  5 21 56  9
D65V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                4                  5
  T2                8                 21
  T3               53                 56
  T4                5                  9
                    vv
clus                 N0 N1 N2
  15Q LOSS MUTATED   32 23 15
  15Q LOSS WILD-TYPE 51 22 17
D65V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               32                 51
  N1               23                 22
  N2               15                 17
                    vv
clus                 M0 M1 M1A MX
  15Q LOSS MUTATED   53 10   0  6
  15Q LOSS WILD-TYPE 70 12   2  7
D65V6, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                53                 70
  M1                10                 12
  M1A                0                  2
  MX                 6                  7
D65V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   27 43
  15Q LOSS WILD-TYPE 47 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     27   43
  15Q LOSS WILD-TYPE   47   45
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               27                 47
  MALE                 43                 45
D65V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   62  5
  15Q LOSS WILD-TYPE 81  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     62    5
  15Q LOSS WILD-TYPE   81    8
                                clus
vv                               15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        62                 81
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
D65V9, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    4 66
  15Q LOSS WILD-TYPE  2 90
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4   66
  15Q LOSS WILD-TYPE    2   90
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 4                  2
  YES               66                 90
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   53  1  4  1
  15Q LOSS WILD-TYPE 68  1  8  2
D65V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               53                 68
  R1                1                  1
  R2                4                  8
  RX                1                  2
D65V11, continuous

Clustering(66) Variable = 16P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     3   1
  16P LOSS WILD-TYPE 114  12
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                126 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 12 
$`16P LOSS MUTATED`
TCGA-DC-6682 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
       13.02         1.02         0.53        18.25 

$`16P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.67        10.39        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.02         6.02         6.94         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        14.01        15.02        36.00         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.41        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.37         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.61        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
        3.39         0.85         2.17         0.39         0.66         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.08         0.76         0.46        55.76        47.08        26.43 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.53               0.39 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             18.25             129.27 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             7.020             10.995 
[1] "0.5 - 18.2 (7.0)"   "0.4 - 129.3 (11.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16P LOSS WILD-TYPE" 
[1] "hr=" "9.1"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16P LOSS MUTATED         0        0         6         0         1         0
  16P LOSS WILD-TYPE      30        8        32         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16P LOSS MUTATED            0          0          1        1         0
  16P LOSS WILD-TYPE          9         23         13       16         9
D66V3, multiclass
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     0   1   8   0
  16P LOSS WILD-TYPE   9  28 101  14
D66V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3                8                101
  T4                0                 14
                    vv
clus                 N0 N1 N2
  16P LOSS MUTATED    6  0  3
  16P LOSS WILD-TYPE 77 45 29
D66V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                6                 77
  N1                0                 45
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  16P LOSS MUTATED     8   1   0   0
  16P LOSS WILD-TYPE 115  21   2  13
D66V6, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                 8                115
  M1                 1                 21
  M1A                0                  2
  MX                 0                 13
D66V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    5  4
  16P LOSS WILD-TYPE 69 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    4
  16P LOSS WILD-TYPE   69   84
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                5                 69
  MALE                  4                 84
D66V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7   1
  16P LOSS WILD-TYPE 136  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    1
  16P LOSS WILD-TYPE  136   12
                                clus
vv                               16P LOSS MUTATED 16P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         7                136
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D66V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   9
  16P LOSS WILD-TYPE   6 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    9
  16P LOSS WILD-TYPE    6  147
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                  6
  YES                9                147
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED     7   0   0   0
  16P LOSS WILD-TYPE 114   2  12   3
D66V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                7                114
  R1                0                  2
  R2                0                 12
  RX                0                  3
D66V11, continuous

Clustering(67) Variable = 16Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     7   1
  16Q LOSS WILD-TYPE 110  12
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                122 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 12 
$`16Q LOSS MUTATED`
TCGA-AF-6672 TCGA-AG-3726 TCGA-AG-3883 TCGA-DC-6682 TCGA-DY-A1DE TCGA-F5-6811 
       10.39         7.96         1.02        13.02       129.27         1.02 
TCGA-F5-6814 TCGA-G5-6233 
        0.53        18.25 

$`16Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        25.02        10.39        14.50         8.45        15.35 
TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       11.67        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        1.02         0.99         0.99         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        0.99         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
        1.02         1.02         1.02         1.02         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.91         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       13.02         1.02         1.02        12.00        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        14.01 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        36.00         6.97        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.41        41.33        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.58         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.37         8.61        11.51        10.78        13.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         3.39         0.85         2.17         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.69         1.08         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.53               0.39 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            129.27             126.41 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             9.175             11.260 
[1] "0.5 - 129.3 (9.2)"  "0.4 - 126.4 (11.3)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16Q LOSS MUTATED         3        0         7         0         1         0
  16Q LOSS WILD-TYPE      27        8        31         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16Q LOSS MUTATED            0          0          2        2         0
  16Q LOSS WILD-TYPE          9         23         12       15         9
D67V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED    0  4 10  1
  16Q LOSS WILD-TYPE  9 25 99 13
D67V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                  9
  T2                4                 25
  T3               10                 99
  T4                1                 13
                    vv
clus                 N0 N1 N2
  16Q LOSS MUTATED   10  0  5
  16Q LOSS WILD-TYPE 73 45 27
D67V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               10                 73
  N1                0                 45
  N2                5                 27
                    vv
clus                  M0  M1 M1A  MX
  16Q LOSS MUTATED    13   1   0   1
  16Q LOSS WILD-TYPE 110  21   2  12
D67V6, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                13                110
  M1                 1                 21
  M1A                0                  2
  MX                 1                 12
D67V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    8  7
  16Q LOSS WILD-TYPE 66 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8    7
  16Q LOSS WILD-TYPE   66   81
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                 66
  MALE                  7                 81
D67V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    13   1
  16Q LOSS WILD-TYPE 130  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     13    1
  16Q LOSS WILD-TYPE  130   12
                                clus
vv                               16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        13                130
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D67V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  14
  16Q LOSS WILD-TYPE   5 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   14
  16Q LOSS WILD-TYPE    5  142
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  5
  YES               14                142
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    11   0   0   0
  16Q LOSS WILD-TYPE 110   2  12   3
D67V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               11                110
  R1                0                  2
  R2                0                 12
  RX                0                  3
D67V11, continuous

Clustering(68) Variable = 17P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   75  8
  17P LOSS WILD-TYPE 42  5
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                83                 47 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 8                  5 
$`17P LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3581 
       25.02        14.50        15.35        11.67        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        1.02         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        1.02         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.91         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        1.02        12.00        12.00        70.03        63.98        51.98 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
        1.94        40.96         0.49         0.69         0.72         4.60 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 
       10.19         6.02         6.02         6.94        13.97         7.99 
TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 
       11.01        14.01         6.97        30.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.41        41.33        57.24       129.27        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        0.49         2.40        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 
       16.34        16.31        16.37        11.51        10.78        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
        8.45         3.39         0.85         2.17         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         0.76         0.46        55.76 

$`17P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3586 
       24.13        10.39         8.45        10.39         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        1.02         0.99         0.99         0.92         1.02         0.99 
TCGA-AG-3896 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 
        1.02         0.99        20.94        13.02         1.02        10.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6903 
       49.94        38.93        61.94        38.01         1.45         1.81 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
        9.37         4.70        60.00        10.98        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1H8 
       12.00        15.02        36.00        12.95        13.02        32.58 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       20.55        19.96        15.85         8.61        13.61        17.46 
TCGA-F5-6811 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        1.02         1.08        18.25        47.08        26.43 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.39               0.92 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            129.27              61.94 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.78              12.00 
[1] "0.4 - 129.3 (10.8)" "0.9 - 61.9 (12.0)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17P LOSS MUTATED        14        5        29         2         1         3
  17P LOSS WILD-TYPE      16        3         9         0         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17P LOSS MUTATED            5         15         10       12         6
  17P LOSS WILD-TYPE          4          8          4        5         3
D68V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    2 17 74 11
  17P LOSS WILD-TYPE  7 12 35  3
D68V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                2                  7
  T2               17                 12
  T3               74                 35
  T4               11                  3
                    vv
clus                 N0 N1 N2
  17P LOSS MUTATED   53 30 20
  17P LOSS WILD-TYPE 30 15 12
D68V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               53                 30
  N1               30                 15
  N2               20                 12
                    vv
clus                 M0 M1 M1A MX
  17P LOSS MUTATED   78 16   0  9
  17P LOSS WILD-TYPE 45  6   2  4
D68V6, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                78                 45
  M1                16                  6
  M1A                0                  2
  MX                 9                  4
D68V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   48 56
  17P LOSS WILD-TYPE 26 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     48   56
  17P LOSS WILD-TYPE   26   32
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               48                 26
  MALE                 56                 32
D68V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   94  6
  17P LOSS WILD-TYPE 49  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     94    6
  17P LOSS WILD-TYPE   49    7
                                clus
vv                               17P LOSS MUTATED 17P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        94                 49
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
D68V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 100
  17P LOSS WILD-TYPE   2  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  100
  17P LOSS WILD-TYPE    2   56
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                  2
  YES              100                 56
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   74  2  9  2
  17P LOSS WILD-TYPE 47  0  3  1
D68V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               74                 47
  R1                2                  0
  R2                9                  3
  RX                2                  1
D68V11, continuous

Clustering(69) Variable = 17Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   19  3
  17Q LOSS WILD-TYPE 98 10
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                22                108 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 10 
$`17Q LOSS MUTATED`
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A00H 
       14.50        15.35         1.02         1.02        13.91        25.94 
TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A02X TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6158 
       12.00        51.98        40.96        10.19        14.01         6.97 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 
       24.13         0.49         2.40        17.69        16.37        11.51 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6814 TCGA-G5-6235 
        2.17         0.66         0.53        55.76 

$`17Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       12.72        25.02        10.39         8.45        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
       12.00         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
        1.02         1.02         1.02         0.99        20.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        63.98        10.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.93        61.94        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.70        13.97        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.02        10.06         5.29       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.33        57.24       129.27        51.48        32.58        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.31         8.61        10.78        13.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        8.45         3.39         0.85         0.39         1.02         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        1.08         0.76         0.46        18.25        47.08        26.43 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.49               0.39 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             55.76             129.27 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            12.955             10.880 
[1] "0.5 - 55.8 (13.0)"  "0.4 - 129.3 (10.9)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "17Q LOSS MUTATED"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17Q LOSS MUTATED         3        0         6         1         1         0
  17Q LOSS WILD-TYPE      27        8        32         1         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17Q LOSS MUTATED            2          5          2        3         2
  17Q LOSS WILD-TYPE          7         18         12       14         7
D69V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    0  5 17  3
  17Q LOSS WILD-TYPE  9 24 92 11
D69V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                  9
  T2                5                 24
  T3               17                 92
  T4                3                 11
                    vv
clus                 N0 N1 N2
  17Q LOSS MUTATED   11  9  5
  17Q LOSS WILD-TYPE 72 36 27
D69V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               11                 72
  N1                9                 36
  N2                5                 27
                    vv
clus                  M0  M1 M1A  MX
  17Q LOSS MUTATED    17   4   0   3
  17Q LOSS WILD-TYPE 106  18   2  10
D69V6, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                17                106
  M1                 4                 18
  M1A                0                  2
  MX                 3                 10
D69V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    9 16
  17Q LOSS WILD-TYPE 65 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      9   16
  17Q LOSS WILD-TYPE   65   72
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                9                 65
  MALE                 16                 72
D69V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    23   1
  17Q LOSS WILD-TYPE 120  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     23    1
  17Q LOSS WILD-TYPE  120   12
                                clus
vv                               17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        23                120
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D69V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  23
  17Q LOSS WILD-TYPE   4 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   23
  17Q LOSS WILD-TYPE    4  133
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 2                  4
  YES               23                133
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    19   1   3   0
  17Q LOSS WILD-TYPE 102   1   9   3
D69V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               19                102
  R1                1                  1
  R2                3                  9
  RX                0                  3
D69V11, continuous

Clustering(70) Variable = 18P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   93 10
  18P LOSS WILD-TYPE 24  3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               103                 27 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                  3 
$`18P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        17.95        17.23        10.62        13.55        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 
       25.02        10.39        14.50        15.35        11.67        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3605 TCGA-AG-3726 
        1.02         1.02         2.01         1.02         0.99         7.96 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 
        1.02         0.99         1.02         0.92         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 
        1.02         1.02         1.02         1.02         0.99        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.94        23.01        17.03        15.91         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        12.00        70.03        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        40.96        38.01         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.70        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        14.01        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
        6.97        30.05        12.95        13.02        10.06       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.33        57.24       129.27        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        2.40        20.55        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.37        11.51        10.78        13.61 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         3.39         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.69         0.76         0.46        18.25        55.76 
TCGA-G5-6641 
       26.43 

$`18P LOSS WILD-TYPE`
TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3727 
       19.10         8.45        10.39         1.02         0.99         0.95 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A01Y 
        0.99         1.02         0.99        20.94        13.02        63.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 
       49.94        38.93        61.94         1.45         1.81         5.29 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       32.58        19.96        20.91         8.61        17.46         8.45 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 
        0.53         1.08        47.08 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.39               0.53 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            129.27              63.98 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             11.51               8.61 
[1] "0.4 - 129.3 (11.5)" "0.5 - 64.0 (8.6)"  
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "18P LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "18P LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "18P LOSS MUTATED" 
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18P LOSS MUTATED        21        5        30         2         2         2
  18P LOSS WILD-TYPE       9        3         8         0         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18P LOSS MUTATED            6         20         11       14         8
  18P LOSS WILD-TYPE          3          3          3        3         1
D70V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    5 21 87 11
  18P LOSS WILD-TYPE  4  8 22  3
D70V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                5                  4
  T2               21                  8
  T3               87                 22
  T4               11                  3
                    vv
clus                 N0 N1 N2
  18P LOSS MUTATED   61 37 25
  18P LOSS WILD-TYPE 22  8  7
D70V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               61                 22
  N1               37                  8
  N2               25                  7
                    vv
clus                 M0 M1 M1A MX
  18P LOSS MUTATED   92 20   2  9
  18P LOSS WILD-TYPE 31  2   0  4
D70V6, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                92                 31
  M1                20                  2
  M1A                2                  0
  MX                 9                  4
D70V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   56 68
  18P LOSS WILD-TYPE 18 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     56   68
  18P LOSS WILD-TYPE   18   20
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               56                 18
  MALE                 68                 20
D70V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   115   7
  18P LOSS WILD-TYPE  28   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    115    7
  18P LOSS WILD-TYPE   28    6
                                clus
vv                               18P LOSS MUTATED 18P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       115                 28
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
D70V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     5 119
  18P LOSS WILD-TYPE   1  37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5  119
  18P LOSS WILD-TYPE    1   37
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 5                  1
  YES              119                 37
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   92  2 11  2
  18P LOSS WILD-TYPE 29  0  1  1
D70V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               92                 29
  R1                2                  0
  R2               11                  1
  RX                2                  1
D70V11, continuous

Clustering(71) Variable = 18Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   98 11
  18Q LOSS WILD-TYPE 19  2
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               109                 21 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                  2 
$`18Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       12.72        25.02        10.39        14.50        15.35        11.67 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3605 
       12.00         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 
        7.96         0.95         1.02         0.99         1.02         0.92 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       15.91         1.02         1.02        12.00        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 
       63.98        10.98        51.98         1.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
        0.49         0.69         0.72         4.60        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.94         9.37         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       14.01        15.02        36.00         6.97        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.02        10.06       126.41        41.33        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.37        11.51        10.78        13.61        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        3.39         0.85         2.17         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76         0.46        18.25        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`18Q LOSS WILD-TYPE`
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3878 TCGA-AG-3892 
        8.45        10.39         1.02         0.99         0.99         1.02 
TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
        0.99        20.94        13.02        49.94        38.93        61.94 
TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 
        1.45         1.81         5.29        32.58        19.96         8.61 
TCGA-EI-6917 TCGA-F5-6814 TCGA-F5-6861 
       17.46         0.53         1.08 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.39               0.53 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            129.27              61.94 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             11.67               8.45 
[1] "0.4 - 129.3 (11.7)" "0.5 - 61.9 (8.4)"  
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-G5-6641 
  "18Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-G5-6641 
  "18Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-G5-6641 
  "18Q LOSS MUTATED" 
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18Q LOSS MUTATED        22        6        34         2         2         3
  18Q LOSS WILD-TYPE       8        2         4         0         0         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18Q LOSS MUTATED            6         21         11       15         9
  18Q LOSS WILD-TYPE          3          2          3        2         0
D71V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    5 22 95 12
  18Q LOSS WILD-TYPE  4  7 14  2
D71V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                5                  4
  T2               22                  7
  T3               95                 14
  T4               12                  2
                    vv
clus                 N0 N1 N2
  18Q LOSS MUTATED   67 39 27
  18Q LOSS WILD-TYPE 16  6  5
D71V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               67                 16
  N1               39                  6
  N2               27                  5
                    vv
clus                  M0  M1 M1A  MX
  18Q LOSS MUTATED   100  21   2  10
  18Q LOSS WILD-TYPE  23   1   0   3
D71V6, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               100                 23
  M1                21                  1
  M1A                2                  0
  MX                10                  3
D71V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   63 72
  18Q LOSS WILD-TYPE 11 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     63   72
  18Q LOSS WILD-TYPE   11   16
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               63                 11
  MALE                 72                 16
D71V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   121  10
  18Q LOSS WILD-TYPE  22   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    121   10
  18Q LOSS WILD-TYPE   22    3
                                clus
vv                               18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       121                 22
  RECTAL MUCINOUS ADENOCARCINOMA               10                  3
D71V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     5 130
  18Q LOSS WILD-TYPE   1  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5  130
  18Q LOSS WILD-TYPE    1   26
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 5                  1
  YES              130                 26
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   100   2  11   2
  18Q LOSS WILD-TYPE  21   0   1   1
D71V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              100                 21
  R1                2                  0
  R2               11                  1
  RX                2                  1
D71V11, continuous

Clustering(72) Variable = 19P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    15   3
  19P LOSS WILD-TYPE 102  10
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                18                112 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 10 
$`19P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-4008 TCGA-AG-A016 TCGA-AG-A01Y TCGA-AG-A020 
       24.13        14.50         1.02         1.02        63.98        10.98 
TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6155 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
        4.70        12.99        14.01        24.13        51.48         0.49 
TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6233 
       16.34        11.51        11.97         0.85         2.17        18.25 

$`19P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       25.02        10.39         8.45        15.35        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       12.00         1.02         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
        1.02         1.02         1.02         1.02         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.91         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 
       13.02         1.02        12.00        12.00        70.03        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
       10.19         6.02         6.02         6.94         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       60.00         7.99        10.98        11.01        15.02        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         6.97        30.05        12.95        13.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.41        41.33        57.24       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.58         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.31        16.37         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6810 
       10.78        13.61        17.46         8.45         3.39         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.49               0.39 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             63.98             129.27 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             12.48              10.70 
[1] "0.5 - 64.0 (12.5)"  "0.4 - 129.3 (10.7)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19P LOSS MUTATED         1        1         6         1         2         2
  19P LOSS WILD-TYPE      29        7        32         1         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19P LOSS MUTATED            1          2          2        2         3
  19P LOSS WILD-TYPE          8         21         12       15         6
D72V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    0  2 19  2
  19P LOSS WILD-TYPE  9 27 90 12
D72V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                0                  9
  T2                2                 27
  T3               19                 90
  T4                2                 12
                    vv
clus                 N0 N1 N2
  19P LOSS MUTATED   10  6  7
  19P LOSS WILD-TYPE 73 39 25
D72V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               10                 73
  N1                6                 39
  N2                7                 25
                    vv
clus                  M0  M1 M1A  MX
  19P LOSS MUTATED    18   4   0   1
  19P LOSS WILD-TYPE 105  18   2  12
D72V6, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                18                105
  M1                 4                 18
  M1A                0                  2
  MX                 1                 12
D72V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   12 11
  19P LOSS WILD-TYPE 62 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     12   11
  19P LOSS WILD-TYPE   62   77
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               12                 62
  MALE                 11                 77
D72V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    20   1
  19P LOSS WILD-TYPE 123  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     20    1
  19P LOSS WILD-TYPE  123   12
                                clus
vv                               19P LOSS MUTATED 19P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        20                123
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D72V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  22
  19P LOSS WILD-TYPE   5 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   22
  19P LOSS WILD-TYPE    5  134
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 1                  5
  YES               22                134
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    18   0   1   0
  19P LOSS WILD-TYPE 103   2  11   3
D72V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               18                103
  R1                0                  2
  R2                1                 11
  RX                0                  3
D72V11, continuous

Clustering(73) Variable = 19Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    14   2
  19Q LOSS WILD-TYPE 103  11
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                16                114 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 11 
$`19Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-4001 TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A020 
       24.13        14.50         1.02        17.03        63.98        10.98 
TCGA-CI-6624 TCGA-DC-5869 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 
        4.70        12.99        24.13         0.49        16.34        11.51 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6233 
       11.97         0.85         2.17        18.25 

$`19Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       25.02        10.39         8.45        15.35        11.67        10.39 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       12.00         1.02         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
        1.02         1.02         1.02         1.02         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       13.91         6.02        25.94        23.01        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 
        1.02         1.02        12.00        12.00        70.03        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
       10.19         6.02         6.02         6.94         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       60.00         7.99        10.98        11.01        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       14.01        15.02        36.00         6.97        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.02        10.06         5.29       126.41        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      129.27        51.48        32.58         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       16.37         8.61        10.78        13.61        17.46         8.45 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        3.39         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.08         0.76         0.46        55.76        47.08        26.43 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.39 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             63.98             129.27 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             12.48              10.70 
[1] "0.5 - 64.0 (12.5)"  "0.4 - 129.3 (10.7)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19Q LOSS MUTATED         1        1         6         1         2         2
  19Q LOSS WILD-TYPE      29        7        32         1         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19Q LOSS MUTATED            0          2          2        1         2
  19Q LOSS WILD-TYPE          9         21         12       16         7
D73V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    0  1 17  2
  19Q LOSS WILD-TYPE  9 28 92 12
D73V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3               17                 92
  T4                2                 12
                    vv
clus                 N0 N1 N2
  19Q LOSS MUTATED   10  4  6
  19Q LOSS WILD-TYPE 73 41 26
D73V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               10                 73
  N1                4                 41
  N2                6                 26
                    vv
clus                  M0  M1 M1A  MX
  19Q LOSS MUTATED    17   2   0   1
  19Q LOSS WILD-TYPE 106  20   2  12
D73V6, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                17                106
  M1                 2                 20
  M1A                0                  2
  MX                 1                 12
D73V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   11  9
  19Q LOSS WILD-TYPE 63 79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     11    9
  19Q LOSS WILD-TYPE   63   79
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               11                 63
  MALE                  9                 79
D73V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    17   1
  19Q LOSS WILD-TYPE 126  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     17    1
  19Q LOSS WILD-TYPE  126   12
                                clus
vv                               19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        17                126
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
D73V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  19
  19Q LOSS WILD-TYPE   5 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   19
  19Q LOSS WILD-TYPE    5  137
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 1                  5
  YES               19                137
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    17   0   0   0
  19Q LOSS WILD-TYPE 104   2  12   3
D73V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               17                104
  R1                0                  2
  R2                0                 12
  RX                0                  3
D73V11, continuous

Clustering(74) Variable = 20P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    14   4
  20P LOSS WILD-TYPE 103   9
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                112 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                  9 
$`20P LOSS MUTATED`
TCGA-AF-4110 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       14.50         0.99        13.91         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-DC-4749 TCGA-DC-6683 
       70.03        63.98         1.94        38.93        11.01        10.06 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-EI-6881 TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6641 
       41.33        57.24        16.37         0.85         2.17        26.43 

$`20P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        25.02        10.39         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       10.39        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.94         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       13.02         1.02        10.98        51.98        49.94        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       40.96        38.01         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.70        13.97        60.00         7.99        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        14.01        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
        6.97        30.05        12.95        13.02         5.29       126.41 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.58         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6810 
       13.61        17.46        11.97         8.45         3.39         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.08         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.46        18.25        55.76        47.08 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.85               0.39 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             70.03             129.27 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            12.955             10.700 
[1] "0.8 - 70.0 (13.0)"  "0.4 - 129.3 (10.7)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "20P LOSS MUTATED"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "20P LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "20P LOSS MUTATED"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "20P LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "20P LOSS MUTATED"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "20P LOSS MUTATED" 
[1] "hr=" "1.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20P LOSS MUTATED         2        5         5         0         0         0
  20P LOSS WILD-TYPE      28        3        33         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20P LOSS MUTATED            2          4          2        2         2
  20P LOSS WILD-TYPE          7         19         12       15         7
D74V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    1  4 16  3
  20P LOSS WILD-TYPE  8 25 93 11
D74V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                1                  8
  T2                4                 25
  T3               16                 93
  T4                3                 11
                    vv
clus                 N0 N1 N2
  20P LOSS MUTATED   13  8  3
  20P LOSS WILD-TYPE 70 37 29
D74V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               13                 70
  N1                8                 37
  N2                3                 29
                    vv
clus                  M0  M1 M1A  MX
  20P LOSS MUTATED    19   3   0   2
  20P LOSS WILD-TYPE 104  19   2  11
D74V6, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                19                104
  M1                 3                 19
  M1A                0                  2
  MX                 2                 11
D74V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   12 12
  20P LOSS WILD-TYPE 62 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12   12
  20P LOSS WILD-TYPE   62   76
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               12                 62
  MALE                 12                 76
D74V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    20   3
  20P LOSS WILD-TYPE 123  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     20    3
  20P LOSS WILD-TYPE  123   10
                                clus
vv                               20P LOSS MUTATED 20P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        20                123
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
D74V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  24
  20P LOSS WILD-TYPE   6 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   24
  20P LOSS WILD-TYPE    6  132
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  6
  YES               24                132
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    18   1   3   0
  20P LOSS WILD-TYPE 103   1   9   3
D74V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               18                103
  R1                1                  1
  R2                3                  9
  RX                0                  3
D74V11, continuous

Clustering(75) Variable = 21Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   43  7
  21Q LOSS WILD-TYPE 74  6
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                50                 80 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 7                  6 
$`21Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       24.13        17.95        17.23        14.50        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3599 
       10.39        12.00         1.02         1.02         1.02         0.99 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        1.02         1.02        12.00        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6643 TCGA-CI-6624 
       10.98        38.93        61.94        40.96         0.69         4.70 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        14.01         6.97        13.02        10.06 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
      126.41        57.24       129.27        51.48        32.58        20.55 
TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
       20.91        15.85        17.69        16.34        16.37        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
        8.45         0.85         0.39         0.66         0.53         0.76 
TCGA-G5-6233 TCGA-G5-6641 
       18.25        26.43 

$`21Q LOSS WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       10.62        13.55        19.10        12.72        25.02        10.39 
TCGA-AF-5654 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        8.45         2.01         1.02         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 
        0.99         0.99         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A023 TCGA-AG-A025 
       15.91        13.02         1.02         1.02        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
        1.94        38.01         0.49         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.00         7.99        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC 
       15.02        36.00        30.05        12.95         5.29        41.33 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       24.13         0.49         2.40        19.96        17.00        18.28 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.61        17.46 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
        3.39         2.17         1.02         0.69         1.08         0.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.39               0.46 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            129.27              60.00 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            13.495              8.530 
[1] "0.4 - 129.3 (13.5)" "0.5 - 60.0 (8.5)"  
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "21Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "21Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "21Q LOSS MUTATED" 
[1] "hr=" "1.1"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  21Q LOSS MUTATED         8        4        15         0         1         3
  21Q LOSS WILD-TYPE      22        4        23         2         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  21Q LOSS MUTATED            6         12          5        7         3
  21Q LOSS WILD-TYPE          3         11          9       10         6
D75V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    1 14 45  4
  21Q LOSS WILD-TYPE  8 15 64 10
D75V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                1                  8
  T2               14                 15
  T3               45                 64
  T4                4                 10
                    vv
clus                 N0 N1 N2
  21Q LOSS MUTATED   28 23 13
  21Q LOSS WILD-TYPE 55 22 19
D75V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               28                 55
  N1               23                 22
  N2               13                 19
                    vv
clus                 M0 M1 M1A MX
  21Q LOSS MUTATED   52  7   0  5
  21Q LOSS WILD-TYPE 71 15   2  8
D75V6, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                52                 71
  M1                 7                 15
  M1A                0                  2
  MX                 5                  8
D75V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   30 34
  21Q LOSS WILD-TYPE 44 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     30   34
  21Q LOSS WILD-TYPE   44   54
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               30                 44
  MALE                 34                 54
D75V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   58  3
  21Q LOSS WILD-TYPE 85 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     58    3
  21Q LOSS WILD-TYPE   85   10
                                clus
vv                               21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        58                 85
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
D75V9, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3 61
  21Q LOSS WILD-TYPE  3 95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3   61
  21Q LOSS WILD-TYPE    3   95
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 3                  3
  YES               61                 95
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   49  0  4  0
  21Q LOSS WILD-TYPE 72  2  8  3
D75V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               49                 72
  R1                0                  2
  R2                4                  8
  RX                0                  3
D75V11, continuous

Clustering(76) Variable = 22Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   35  6
  22Q LOSS WILD-TYPE 82  7
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                41                 89 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 6                  7 
$`22Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 
       13.55        14.50        15.35        10.39        12.00         1.02 
TCGA-AG-3583 TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H 
        2.01         1.02         1.02         1.02         1.02        25.94 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6644 
       12.00        10.98         1.94        38.93         0.49         0.72 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-5869 
       10.19         6.02         4.70        13.97        10.98        12.99 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC 
       14.01         6.97        30.05        13.02        10.06        41.33 
TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6881 TCGA-F5-6702 
       51.48         2.40        20.55        17.69        16.37         2.17 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        0.39         0.66         0.76        18.25        26.43 

$`22Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        10.62        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3582 TCGA-AG-3586 
       25.02        10.39         8.45        11.67         1.02         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
        1.02         0.99         0.99         7.96         0.95         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        0.99         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         0.99        20.94        13.91         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       12.00        70.03        63.98        51.98        49.94        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       40.96        38.01         1.45         0.69         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        6.02         6.94         9.37        60.00         7.99        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 
       15.02        12.00        15.02        36.00        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.41        57.24       129.27        24.13        32.58         0.49 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 
       11.97         8.45         3.39         0.85         1.02         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.08         0.46        55.76        47.08 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.39               0.46 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             51.48             129.27 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             10.98              11.51 
[1] "0.4 - 51.5 (11.0)"  "0.5 - 129.3 (11.5)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "22Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "22Q LOSS MUTATED" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
  "22Q LOSS MUTATED" 
[1] "hr=" "4.7"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  22Q LOSS MUTATED         6        2        14         0         1         3
  22Q LOSS WILD-TYPE      24        6        24         2         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  22Q LOSS MUTATED            4         12          2        7         3
  22Q LOSS WILD-TYPE          5         11         12       10         6
D76V3, multiclass
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    1  8 42  5
  22Q LOSS WILD-TYPE  8 21 67  9
D76V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                1                  8
  T2                8                 21
  T3               42                 67
  T4                5                  9
                    vv
clus                 N0 N1 N2
  22Q LOSS MUTATED   22 24  9
  22Q LOSS WILD-TYPE 61 21 23
D76V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               22                 61
  N1               24                 21
  N2                9                 23
                    vv
clus                 M0 M1 M1A MX
  22Q LOSS MUTATED   40  9   0  6
  22Q LOSS WILD-TYPE 83 13   2  7
D76V6, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                40                 83
  M1                 9                 13
  M1A                0                  2
  MX                 6                  7
D76V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   24 32
  22Q LOSS WILD-TYPE 50 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   32
  22Q LOSS WILD-TYPE   50   56
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               24                 50
  MALE                 32                 56
D76V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   50  4
  22Q LOSS WILD-TYPE 93  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     50    4
  22Q LOSS WILD-TYPE   93    9
                                clus
vv                               22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        50                 93
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
D76V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3  53
  22Q LOSS WILD-TYPE   3 103
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   53
  22Q LOSS WILD-TYPE    3  103
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                  3
  YES               53                103
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   40  1  5  0
  22Q LOSS WILD-TYPE 81  1  7  3
D76V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               40                 81
  R1                1                  1
  R2                5                  7
  RX                0                  3
D76V11, continuous

Clustering(77) Variable = XQ LOSS MUTATION ANALYSIS
D77V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    15   1
  XQ LOSS WILD-TYPE 102  12
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               16               114 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                12 
$`XQ LOSS MUTATED`
TCGA-AF-2693 TCGA-AG-3575 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A01N TCGA-AG-A01Y 
       19.10        12.00        13.91        23.01        12.00        63.98 
TCGA-AG-A02X TCGA-AH-6544 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 
       40.96         0.49        10.19        14.01        30.05         5.29 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-7002 TCGA-F5-6571 
      129.27        32.58        11.97         0.85 

$`XQ LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        17.95        17.23        10.62        13.55        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       25.02        10.39        14.50         8.45        15.35        11.67 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       10.39         1.02         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.94         6.02        25.94        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 
        1.02         1.02        12.00        70.03        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       49.94         1.94        38.93        61.94        38.01         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         4.60         1.81         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       10.98        11.01        15.02        12.99        12.00        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       36.00         6.97        12.95        13.02        10.06       126.41 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       41.33        57.24        24.13        51.48         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.37         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6702 
       10.78        13.61        17.46         8.45         3.39         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        55.76        47.08        26.43 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.49              0.39 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           129.27            126.41 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           13.960            10.505 
[1] "0.5 - 129.3 (14.0)" "0.4 - 126.4 (10.5)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "3"  
D77V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XQ LOSS MUTATED         5        3         7         0         0         0
  XQ LOSS WILD-TYPE      25        5        31         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XQ LOSS MUTATED            2          1          2        4         0
  XQ LOSS WILD-TYPE          7         22         12       13         9
D77V3, multiclass
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    0  8 17  0
  XQ LOSS WILD-TYPE  9 21 92 14
D77V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0                 9
  T2               8                21
  T3              17                92
  T4               0                14
                   vv
clus                N0 N1 N2
  XQ LOSS MUTATED   16  4  5
  XQ LOSS WILD-TYPE 67 41 27
D77V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              16                67
  N1               4                41
  N2               5                27
                   vv
clus                 M0  M1 M1A  MX
  XQ LOSS MUTATED    18   5   0   1
  XQ LOSS WILD-TYPE 105  17   2  12
D77V6, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               18               105
  M1                5                17
  M1A               0                 2
  MX                1                12
D77V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   14 11
  XQ LOSS WILD-TYPE 60 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14   11
  XQ LOSS WILD-TYPE   60   77
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              14                60
  MALE                11                77
D77V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    21   3
  XQ LOSS WILD-TYPE 122  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     21    3
  XQ LOSS WILD-TYPE  122   10
                                clus
vv                               XQ LOSS MUTATED XQ LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       21               122
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
D77V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  24
  XQ LOSS WILD-TYPE   5 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   24
  XQ LOSS WILD-TYPE    5  132
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                1                 5
  YES              24               132
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    17   0   3   1
  XQ LOSS WILD-TYPE 104   2   9   2
D77V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              17               104
  R1               0                 2
  R2               3                 9
  RX               1                 2
D77V11, continuous
> q(save="no")
