
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/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/18/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/18/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/READ-TP/2735961/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/READ-TP/2589030/1.GDAC_clinicalDataPicker.Finished/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=", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=READ-TP"
[1] "opt"  "-OP="
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt" ""   
[1] "dx" ""  

nPatients in clinical file=168, in cluster file=162, common to both=162
[1] "Reduce the number of clustering variables from 80 to 75."
[1]  75 162
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               158 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4               158 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               27               135 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               27               135 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               20               142 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               20               142 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21               141 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               21               141 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17               145 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               17               145 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               23               139 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               23               139 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               158 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               158 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               159 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3               159 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               142 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20               142 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               150 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               150 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               27               135 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               27               135 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27               135 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               27               135 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               90                72 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               90                72 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               79                83 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               79                83 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               27               135 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               27               135 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               72                90 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               72                90 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               35               127 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               35               127 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26               136 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               26               136 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                154 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 8                154 
[1] "10q gain mutation analysis"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                158 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                158 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                21                141 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                21                141 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                145 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                145 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                134 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                134 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                19                143 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                19                143 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               102                 60 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               102                 60 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                158 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                158 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                29                133 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                29                133 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                132 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                132 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                159 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                159 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                144 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                18                144 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                155 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                155 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                158 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                158 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                142 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                142 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                139 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                23                139 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                95                 67 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                95                 67 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               132                 30 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               132                 30 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                155 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                155 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                157 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                157 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               155 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                7               155 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               141 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               21               141 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               155 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7               155 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               157 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5               157 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8               154 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8               154 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               158 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               158 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               39               123 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               39               123 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               46               116 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               46               116 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               151 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               151 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               139 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               139 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               154 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8               154 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14               148 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14               148 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               56               106 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               56               106 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               159 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               159 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               12               150 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               12               150 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               151 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11               151 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                145 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                17                145 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                21                141 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                21                141 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                19                143 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                19                143 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                139 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                139 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                150 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                150 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                154 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                154 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                157 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                157 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                51                111 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                51                111 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                58                104 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                58                104 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                156 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                156 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                152 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                152 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                89                 73 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                89                 73 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                147 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                15                147 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               114                 48 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               114                 48 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               126                 36 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               126                 36 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 7                155 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 7                155 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                155 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                155 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                144 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                18                144 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                119 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                43                119 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                42                120 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                42                120 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               156 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               156 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "PATHOLOGICSPREAD(PT)"                  
[12] "PATHOLOGICSPREAD(PN)"                  
[13] "PATHOLOGICSPREAD(M)"                   
[14] "TUMORSTAGE"                            
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 162 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
         594          482          358          323          412          581 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
         387          536          316          441          257          231 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
         193          223           NA           NA           NA           NA 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
          31           31           61           NA           NA           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           NA           NA           NA 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
          NA           NA           NA           31           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 
          NA           NA           28           NA           31           30 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
          30           NA           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         1581 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1519           59         1184         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 
         304          153          273          224          212          849 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
         212          608          180          121          152            8 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        3635         1257         1741         3683          734         1566 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
         991           15           73          232            5           66 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
         250           14          121           20          210          216 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
         187          108          121           83          159          237 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
          84           62           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         1451           NA          636 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=95,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=41,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.N':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGICSPREAD(M)':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "GENDER"                                
[3] "HISTOLOGICAL.TYPE"                     
[4] "PATHOLOGY.T"                           
[5] "PATHOLOGY.N"                           
[6] "PATHOLOGICSPREAD(M)"                   
[7] "TUMOR.STAGE"                           
[8] "RADIATIONS.RADIATION.REGIMENINDICATION"
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
30 50 50 25 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 162 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=47, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
PATHOLOGY.T, 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"

$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, 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"

$Table
vv
N0 N1 N2 
83 45 32 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
83 45 32 
PATHOLOGICSPREAD(M), nv=4, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE$',vnm)"
vv
  I  II III  IV 
 30  50  50  25 
[1] "table(vv)"
vv
  I  II III  IV 
 30  50  50  25 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 30  50  50  25 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 30  50  50  25 
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     2   1
  1P GAIN WILD-TYPE 112  10
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3               122 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                10 
$`1P GAIN MUTATED`
TCGA-AG-3587 TCGA-DY-A1DF TCGA-EI-7004 
        1.02        24.13         2.04 

$`1P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3599 
        6.35         7.33         1.02         1.02         2.01         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98         7.36         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.92         3.98         5.00         0.26       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.33        57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
        3.98         2.73         5.23         7.79         2.76         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.02              0.16 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            24.13            121.08 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            2.040             6.625 
[1] "1.0 - 24.1 (2.0)"  "0.2 - 121.1 (6.6)"
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"1P GAIN WILD-TYPE" 
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"1P GAIN WILD-TYPE" 
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"1P GAIN WILD-TYPE" 
[1] "hr=" "10" 
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    1
  1P GAIN WILD-TYPE   71   87
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                71
  MALE                 1                87
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    1
  1P GAIN WILD-TYPE  140   12
                                clus
vv                               1P GAIN MUTATED 1P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        3               140
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     0   1   1   2
  1P GAIN WILD-TYPE   9  28 108  12
D1V5, multiclass
                   vv
clus                N0 N1 N2
  1P GAIN MUTATED    1  0  3
  1P GAIN WILD-TYPE 82 45 29
D1V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  1P GAIN MUTATED     4   0   0   0
  1P GAIN WILD-TYPE 119  22   2  13
D1V7, multiclass
                   vv
clus                 I II III IV
  1P GAIN MUTATED    1  0   2  1
  1P GAIN WILD-TYPE 29 50  48 24
D1V8, multiclass
D1V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    4
  1P GAIN WILD-TYPE    6  152
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 6
  YES               4               152

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   18  3
  1Q GAIN WILD-TYPE 96  8
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               21               104 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                 8 
$`1Q GAIN MUTATED`
TCGA-AF-2692 TCGA-AF-6672 TCGA-AG-3587 TCGA-AG-3999 TCGA-AG-A015 TCGA-AG-A01N 
       13.55         7.33         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-DY-A1DF TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-7004 
        0.72         9.37        24.13         3.55         5.23         2.04 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6641 
        0.69         0.76        20.91 

$`1Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       19.53        15.85        11.77        10.62        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         2.01         0.99         1.02         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-4001 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-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.91         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        1.02         1.02        12.00        63.98        10.98        49.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       38.93        61.94        40.96         1.45         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.02         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-5869 
       60.00         7.99        10.98        11.01         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98         7.36         6.97        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       121.08        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 
        7.63         0.16         2.17         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        0.66         6.90         7.10         6.15         3.98         2.73 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        7.79         2.76         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.66         0.53         1.08         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 
       47.70        47.08 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.49              0.16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            70.03            121.08 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            5.230             6.625 
[1] "0.5 - 70.0 (5.2)"  "0.2 - 121.1 (6.6)"
       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-3581        TCGA-AG-3582 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
  "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-3581        TCGA-AG-3582 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
  "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-3581        TCGA-AG-3582 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
  "1Q GAIN MUTATED" 
[1] "hr=" "1.7"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14   13
  1Q GAIN WILD-TYPE   60   75
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              14                60
  MALE                13                75
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     22    4
  1Q GAIN WILD-TYPE  121    9
                                clus
vv                               1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       22               121
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    3  2 15  7
  1Q GAIN WILD-TYPE  6 27 94  7
D2V5, multiclass
                   vv
clus                N0 N1 N2
  1Q GAIN MUTATED   12  5  9
  1Q GAIN WILD-TYPE 71 40 23
D2V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  1Q GAIN MUTATED    20   4   0   3
  1Q GAIN WILD-TYPE 103  18   2  10
D2V7, multiclass
                   vv
clus                 I II III IV
  1Q GAIN MUTATED    3  8   9  5
  1Q GAIN WILD-TYPE 27 42  41 20
D2V8, multiclass
D2V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   26
  1Q GAIN WILD-TYPE    5  130
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                1                 5
  YES              26               130

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED   15  2
  2P GAIN WILD-TYPE 99  9
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               17               108 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                 9 
$`2P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-5654 TCGA-AG-4007 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 
       15.85         8.45         1.02        12.00        70.03        38.01 
TCGA-AH-6897 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-6154 TCGA-DY-A1DE 
        4.60        60.00         7.99        10.98         8.98       121.08 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6514 TCGA-F5-6465 TCGA-G5-6572 
       51.48         7.63         7.10         3.39        47.08 

$`2P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        11.77        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       17.62        10.39        14.50         7.59         6.35         7.33 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        1.02         1.02         2.01         1.02         0.99         1.02 
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-3999 TCGA-AG-4001 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-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y 
       15.91        13.02         1.02         1.02        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-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 
       40.96         0.49         1.45         0.69         0.72         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-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       13.97        11.01         9.99         5.03         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.91         6.97        19.99         5.92         3.98         5.00 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        0.26       119.51        41.33        57.24        24.13        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        3.98         0.66         6.90         6.15         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
        2.73         5.23         7.79         2.76         2.04         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-G5-6641 
        1.08         0.76         0.46        18.25        47.70        20.91 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.02              0.16 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           121.08            119.51 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           10.980             5.575 
[1] "1.0 - 121.1 (11.0)" "0.2 - 119.5 (5.6)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "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-3581        TCGA-AG-3582 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-G5-6641 
"2P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "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-3581        TCGA-AG-3582 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-G5-6641 
"2P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "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-3581        TCGA-AG-3582 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "2P GAIN MUTATED"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-G5-6641 
"2P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15    5
  2P GAIN WILD-TYPE   59   83
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              15                59
  MALE                 5                83
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     20    0
  2P GAIN WILD-TYPE  123   13
                                clus
vv                               2P GAIN MUTATED 2P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       20               123
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    0  3 13  3
  2P GAIN WILD-TYPE  9 26 96 11
D3V5, multiclass
                   vv
clus                N0 N1 N2
  2P GAIN MUTATED   10  3  6
  2P GAIN WILD-TYPE 73 42 26
D3V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  2P GAIN MUTATED    12   5   0   2
  2P GAIN WILD-TYPE 111  17   2  11
D3V7, multiclass
                   vv
clus                 I II III IV
  2P GAIN MUTATED    2  7   5  4
  2P GAIN WILD-TYPE 28 43  45 21
D3V8, multiclass
D3V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0   20
  2P GAIN WILD-TYPE    6  136
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                0                 6
  YES              20               136

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED   16  1
  2Q GAIN WILD-TYPE 98 10
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               17               108 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                10 
$`2Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-5654 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-A01N TCGA-AG-A01W 
       15.85         8.45         1.02         1.02        12.00        70.03 
TCGA-AG-A032 TCGA-AH-6897 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6154 TCGA-DY-A1DE 
       38.01         4.60        60.00         7.99         8.98       121.08 
TCGA-EF-5831 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6863 TCGA-G5-6572 
        2.40         7.10         3.39         0.76        47.08 

$`2Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        11.77        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       17.62        10.39        14.50         7.59         6.35         7.33 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        1.02         1.02         2.01         1.02         0.99         1.02 
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-4001 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
        0.99         0.99         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-A01Y TCGA-AG-A020 
       13.02         1.02         1.02        12.00        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-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 
        0.49         1.45         0.69         0.72         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-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       10.98        11.01         9.99         5.03         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.91         6.97        19.99         5.92         3.98         5.00 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        0.26       119.51        41.33        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.58         0.49         7.63         0.16         2.17         8.22 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
        0.46         3.98         0.66         6.90         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.53         1.08         0.46        18.25        47.70        20.91 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.76              0.16 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           121.08            119.51 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             8.45              6.02 
[1] "0.8 - 121.1 (8.4)" "0.2 - 119.5 (6.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "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 WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-G5-6641 
"2Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "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 WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-G5-6641 
"2Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "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 WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-G5-6641 
"2Q GAIN WILD-TYPE" 
[1] "hr=" "4"  
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     15    6
  2Q GAIN WILD-TYPE   59   82
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              15                59
  MALE                 6                82
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     21    0
  2Q GAIN WILD-TYPE  122   13
                                clus
vv                               2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       21               122
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    0  3 13  4
  2Q GAIN WILD-TYPE  9 26 96 10
D4V5, multiclass
                   vv
clus                N0 N1 N2
  2Q GAIN MUTATED   11  2  7
  2Q GAIN WILD-TYPE 72 43 25
D4V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  2Q GAIN MUTATED    14   4   0   2
  2Q GAIN WILD-TYPE 109  18   2  11
D4V7, multiclass
                   vv
clus                 I II III IV
  2Q GAIN MUTATED    2  8   6  3
  2Q GAIN WILD-TYPE 28 42  44 22
D4V8, multiclass
D4V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   21
  2Q GAIN WILD-TYPE    6  135
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                0                 6
  YES              21               135

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    10   1
  3P GAIN WILD-TYPE 104  10
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               114 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                10 
$`3P GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 
       17.62         6.35         7.33        10.98         5.03         6.97 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-7002 
       41.33       121.08         2.40         0.46         2.76 

$`3P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3581 
       12.72        10.39        14.50         8.45         7.59         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         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-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-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-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 
        7.99        11.01         9.99         8.98         7.36        27.91 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.97        19.99         5.92         3.98         5.00         0.26 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      119.51        57.24        24.13        51.48        32.58         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
        7.63         0.16         2.17         8.22         3.98         0.66 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        6.90         7.10         6.15         3.55         3.98         2.73 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        5.23         7.79         2.04         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        47.70        47.08        20.91 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.46              0.16 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           121.08            119.51 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            6.970             6.085 
[1] "0.5 - 121.1 (7.0)" "0.2 - 119.5 (6.1)"
       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-3581        TCGA-AG-3582 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"3P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      8    9
  3P GAIN WILD-TYPE   66   79
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               8                66
  MALE                 9                79
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     17    0
  3P GAIN WILD-TYPE  126   13
                                clus
vv                               3P GAIN MUTATED 3P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       17               126
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    0  3 12  2
  3P GAIN WILD-TYPE  9 26 97 12
D5V5, multiclass
                   vv
clus                N0 N1 N2
  3P GAIN MUTATED    8  3  6
  3P GAIN WILD-TYPE 75 42 26
D5V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  3P GAIN MUTATED    11   2   1   3
  3P GAIN WILD-TYPE 112  20   1  10
D5V7, multiclass
                   vv
clus                 I II III IV
  3P GAIN MUTATED    1  6   5  5
  3P GAIN WILD-TYPE 29 44  45 20
D5V8, multiclass
D5V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   15
  3P GAIN WILD-TYPE    4  141
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                2                 4
  YES              15               141

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    13   2
  3Q GAIN WILD-TYPE 101   9
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15               110 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 9 
$`3Q GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3726 TCGA-CL-5917 
       17.62        10.39         6.35         7.33         1.02        60.00 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 TCGA-DY-A1DC TCGA-EF-5831 TCGA-EI-6510 
       10.98         5.03         6.97        41.33         2.40         0.46 
TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6863 
        7.10         2.76         0.76 

$`3Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3581 TCGA-AG-3582 
       12.72        14.50         8.45         7.59         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3587 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-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-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-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-5918 TCGA-DC-4749 TCGA-DC-5337 
        9.37         4.70        13.97         7.99        11.01         9.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        8.98         7.36        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
        3.98         5.00         0.26       119.51        57.24       121.08 
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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
        2.17         8.22         3.98         0.66         6.90         6.15 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        3.55         3.98         2.73         5.23         7.79         2.04 
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-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.08         0.46        18.25        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.46              0.16 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            60.00            121.08 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            6.970             6.085 
[1] "0.5 - 60.0 (7.0)"  "0.2 - 121.1 (6.1)"
       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-3581        TCGA-AG-3582 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"3Q GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     13   10
  3Q GAIN WILD-TYPE   61   78
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              13                61
  MALE                10                78
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     23    0
  3Q GAIN WILD-TYPE  120   13
                                clus
vv                               3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       23               120
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    0  4 16  3
  3Q GAIN WILD-TYPE  9 25 93 11
D6V5, multiclass
                   vv
clus                N0 N1 N2
  3Q GAIN MUTATED    9  7  7
  3Q GAIN WILD-TYPE 74 38 25
D6V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  3Q GAIN MUTATED    15   3   1   4
  3Q GAIN WILD-TYPE 108  19   1   9
D6V7, multiclass
                   vv
clus                 I II III IV
  3Q GAIN MUTATED    2  6   9  5
  3Q GAIN WILD-TYPE 28 44  41 20
D6V8, multiclass
D6V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   21
  3Q GAIN WILD-TYPE    4  135
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                2                 4
  YES              21               135

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     3   1
  4P GAIN WILD-TYPE 111  10
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               121 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                10 
$`4P GAIN MUTATED`
TCGA-AG-A011 TCGA-DC-4749 TCGA-DY-A1DG TCGA-EI-6510 
       17.03        11.01        51.48         0.46 

$`4P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.94        23.01        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-5337 TCGA-DC-5869 
       13.97        60.00         7.99        10.98         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98         7.36         6.97        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       121.08        24.13        32.58         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
        7.63         0.16         2.17         8.22         3.98         0.66 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        6.90         7.10         6.15         3.55         3.98         2.73 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
        5.23         7.79         2.76         2.04         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        47.70        47.08 
TCGA-G5-6641 
       20.91 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.46              0.16 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            51.48            121.08 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            14.02              6.15 
[1] "0.5 - 51.5 (14.0)" "0.2 - 121.1 (6.2)"
       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-3581        TCGA-AG-3582 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"4P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    3
  4P GAIN WILD-TYPE   73   85
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                73
  MALE                 3                85
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    0
  4P GAIN WILD-TYPE  139   13
                                clus
vv                               4P GAIN MUTATED 4P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        4               139
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     0   2   2   0
  4P GAIN WILD-TYPE   9  27 107  14
D7V5, multiclass
                   vv
clus                N0 N1 N2
  4P GAIN MUTATED    3  1  0
  4P GAIN WILD-TYPE 80 44 32
D7V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  4P GAIN MUTATED     2   1   0   1
  4P GAIN WILD-TYPE 121  21   2  12
D7V7, multiclass
                   vv
clus                 I II III IV
  4P GAIN MUTATED    1  1   0  2
  4P GAIN WILD-TYPE 29 49  50 23
D7V8, multiclass
D7V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    4
  4P GAIN WILD-TYPE    6  152
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 6
  YES               4               152

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     1   1
  4Q GAIN WILD-TYPE 113  10
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               123 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                10 
$`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 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.92         1.02         0.99         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         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98         7.36         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.92         3.98         5.00         0.26       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       41.33        57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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 
       47.70        47.08        20.91 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.99              0.16 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            51.48            121.08 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           26.235             6.350 
[1] "1.0 - 51.5 (26.2)" "0.2 - 121.1 (6.3)"
       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-3581        TCGA-AG-3582 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-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-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-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-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-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-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"4Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               123 
       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-3581        TCGA-AG-3582 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4022 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L        TCGA-AG-A01N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A023 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544        TCGA-AH-6547 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6622 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957        TCGA-CL-5917 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE        TCGA-DY-A1DF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE   74   85
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               0                74
  MALE                 3                85
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    0
  4Q GAIN WILD-TYPE  140   13
                                clus
vv                               4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        3               140
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     0   0   3   0
  4Q GAIN WILD-TYPE   9  29 106  14
D8V5, multiclass
                   vv
clus                N0 N1 N2
  4Q GAIN MUTATED    1  2  0
  4Q GAIN WILD-TYPE 82 43 32
D8V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  4Q GAIN MUTATED     2   1   0   0
  4Q GAIN WILD-TYPE 121  21   2  13
D8V7, multiclass
                   vv
clus                 I II III IV
  4Q GAIN MUTATED    0  1   1  1
  4Q GAIN WILD-TYPE 30 49  49 24
D8V8, multiclass
D8V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE    6  153
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 6
  YES               3               153

Clustering(9) Variable = 5p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   17  1
  5P GAIN WILD-TYPE 97 10
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               18               107 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                10 
$`5P GAIN MUTATED`
TCGA-AF-3911 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-4007 TCGA-AG-A015 TCGA-AG-A01N 
       17.62         1.02         1.02         1.02        13.02        12.00 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6158 
       38.93        40.96        38.01         0.72         5.03         6.97 
TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6863 
        2.40         7.10         3.98         2.17         1.02         0.76 

$`5P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        7.33         1.02         2.01         0.99         1.02         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-4001 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-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.91         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02         1.02        12.00        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-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         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-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98        11.01         9.99         8.98         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.91        19.99         5.92         3.98         5.00         0.26 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      119.51        41.33        57.24       121.08        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.58         0.49         7.63         0.16         2.17         8.22 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
        0.46         3.98         0.66         6.90         6.15         3.55 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        2.73         5.23         7.79         2.76         2.04         3.39 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.85         0.39         0.66         0.69         0.53         1.08 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.25        47.70        47.08        20.91 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.72              0.16 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            40.96            121.08 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            4.505             6.900 
[1] "0.7 - 41.0 (4.5)"  "0.2 - 121.1 (6.9)"
       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-3581        TCGA-AG-3582 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"5P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      8   12
  5P GAIN WILD-TYPE   66   76
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               8                66
  MALE                12                76
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     20    0
  5P GAIN WILD-TYPE  123   13
                                clus
vv                               5P GAIN MUTATED 5P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       20               123
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    1  5 12  2
  5P GAIN WILD-TYPE  8 24 97 12
D9V5, multiclass
                   vv
clus                N0 N1 N2
  5P GAIN MUTATED    9  7  3
  5P GAIN WILD-TYPE 74 38 29
D9V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  5P GAIN MUTATED    13   5   0   2
  5P GAIN WILD-TYPE 110  17   2  11
D9V7, multiclass
                   vv
clus                 I II III IV
  5P GAIN MUTATED    4  4   6  5
  5P GAIN WILD-TYPE 26 46  44 20
D9V8, multiclass
D9V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   19
  5P GAIN WILD-TYPE    5  137
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                1                 5
  YES              19               137

Clustering(10) Variable = 5q gain mutation analysis
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    10   0
  5Q GAIN WILD-TYPE 104  11
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               10               115 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                11 
$`5Q GAIN MUTATED`
TCGA-AG-3582 TCGA-AG-4007 TCGA-AG-A01N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6644 
        1.02         1.02        12.00        40.96        38.01         0.72 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6811 
        7.10         3.98         2.76         1.02 

$`5Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        6.35         7.33         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
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-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-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       38.93        61.94         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-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 
        9.99         5.03         8.98         7.36         6.97        27.91 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.97        19.99         5.92         3.98         5.00         0.26 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      119.51        41.33        57.24       121.08        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         7.63         0.16         2.17 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
        8.22         0.46         3.98         0.66         6.90         6.15 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
        3.55         2.73         5.23         7.79         2.04         3.39 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        0.85         2.17         0.39         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        47.70        47.08 
TCGA-G5-6641 
       20.91 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.72              0.16 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            40.96            121.08 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             3.37              6.90 
[1] "0.7 - 41.0 (3.4)"  "0.2 - 121.1 (6.9)"
       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-3581        TCGA-AG-3582 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"5Q GAIN WILD-TYPE" 
[1] "hr="     "7.6e+07"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    7
  5Q GAIN WILD-TYPE   69   81
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               5                69
  MALE                 7                81
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     12    0
  5Q GAIN WILD-TYPE  131   13
                                clus
vv                               5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       12               131
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED     0   2   9   1
  5Q GAIN WILD-TYPE   9  27 100  13
D10V5, multiclass
                   vv
clus                N0 N1 N2
  5Q GAIN MUTATED    5  3  3
  5Q GAIN WILD-TYPE 78 42 29
D10V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  5Q GAIN MUTATED     7   4   0   1
  5Q GAIN WILD-TYPE 116  18   2  12
D10V7, multiclass
                   vv
clus                 I II III IV
  5Q GAIN MUTATED    1  3   3  4
  5Q GAIN WILD-TYPE 29 47  47 21
D10V8, multiclass
D10V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   12
  5Q GAIN WILD-TYPE    6  144
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 6
  YES              12               144

Clustering(11) Variable = 6p gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   18  1
  6P GAIN WILD-TYPE 96 10
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               19               106 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                10 
$`6P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AG-4007 TCGA-AG-4022 
       19.53        17.62        10.39         7.59         1.02         0.99 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-5869 
       13.02         1.02        12.00         0.72         9.37         5.03 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 
        8.98        27.91       121.08         3.98         0.66         3.39 
TCGA-F5-6810 
        0.39 

$`6P GAIN WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       15.85        11.77        10.62        13.55        19.10        12.72 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 
       14.50         8.45         6.35         7.33         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        2.01         1.02         0.99         1.02         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-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         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-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.94         4.70        13.97        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       11.01         9.99         7.36         6.97         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24        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-6513 
        7.63         0.16         2.17         8.22         0.46         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        7.79         2.76         2.04         0.85         2.17         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        47.70        47.08        20.91 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.39              0.16 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           121.08            119.51 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             7.59              6.25 
[1] "0.4 - 121.1 (7.6)" "0.2 - 119.5 (6.2)"
       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 WILD-TYPE" 
       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 WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"6P GAIN WILD-TYPE" 
       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 WILD-TYPE" 
       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 WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"6P GAIN WILD-TYPE" 
       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 WILD-TYPE" 
       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 WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"6P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     13   14
  6P GAIN WILD-TYPE   61   74
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              13                61
  MALE                14                74
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     27    0
  6P GAIN WILD-TYPE  116   13
                                clus
vv                               6P GAIN MUTATED 6P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       27               116
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    2  4 18  3
  6P GAIN WILD-TYPE  7 25 91 11
D11V5, multiclass
                   vv
clus                N0 N1 N2
  6P GAIN MUTATED   11  8  7
  6P GAIN WILD-TYPE 72 37 25
D11V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  6P GAIN MUTATED    18   6   0   3
  6P GAIN WILD-TYPE 105  16   2  10
D11V7, multiclass
                   vv
clus                 I II III IV
  6P GAIN MUTATED    5  5  10  5
  6P GAIN WILD-TYPE 25 45  40 20
D11V8, multiclass
D11V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3   24
  6P GAIN WILD-TYPE    3  132
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                3                 3
  YES              24               132

Clustering(12) Variable = 6q gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   17  2
  6Q GAIN WILD-TYPE 97  9
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               19               106 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                 9 
$`6Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-4007 TCGA-AG-4022 
       19.53        10.39        14.50         7.59         1.02         0.99 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-5869 
       13.02         1.02        12.00         0.72         9.37         5.03 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 
        8.98        27.91        51.48         3.98         0.66         3.39 
TCGA-F5-6810 
        0.39 

$`6Q GAIN WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       15.85        11.77        10.62        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 
       17.62         8.45         6.35         7.33         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        2.01         1.02         0.99         1.02         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-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         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-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.94         4.70        13.97        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       11.01         9.99         7.36         6.97         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       121.08        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-6513 
        7.63         0.16         2.17         8.22         0.46         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        7.79         2.76         2.04         0.85         2.17         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        47.70        47.08        20.91 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.39              0.16 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            51.48            121.08 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             7.59              6.25 
[1] "0.4 - 51.5 (7.6)"  "0.2 - 121.1 (6.2)"
       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 WILD-TYPE" 
       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 WILD-TYPE" 
       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-3581        TCGA-AG-3582 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" 
       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 WILD-TYPE" 
       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-3581        TCGA-AG-3582 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" 
       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 WILD-TYPE" 
       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-3581        TCGA-AG-3582 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"6Q GAIN WILD-TYPE" 
[1] "hr=" "2.6"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     12   15
  6Q GAIN WILD-TYPE   62   73
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              12                62
  MALE                15                73
D12V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     26    0
  6Q GAIN WILD-TYPE  117   13
                                clus
vv                               6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       26               117
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    2  4 17  4
  6Q GAIN WILD-TYPE  7 25 92 10
D12V5, multiclass
                   vv
clus                N0 N1 N2
  6Q GAIN MUTATED   10  9  7
  6Q GAIN WILD-TYPE 73 36 25
D12V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  6Q GAIN MUTATED    17   7   0   3
  6Q GAIN WILD-TYPE 106  15   2  10
D12V7, multiclass
                   vv
clus                 I II III IV
  6Q GAIN MUTATED    5  4   9  7
  6Q GAIN WILD-TYPE 25 46  41 18
D12V8, multiclass
D12V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   25
  6Q GAIN WILD-TYPE    4  131
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                2                 4
  YES              25               131

Clustering(13) Variable = 7p gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   64  8
  7P GAIN WILD-TYPE 50  3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               72                53 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                 3 
$`7P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       15.85        11.77        17.62        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3742 
        7.59         6.35         1.02         1.02         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3893 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 
        0.99         0.99         1.02         1.02         0.99        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A026 
       13.02         1.02         1.02        12.00        70.03         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 
       38.93        38.01         0.69         0.72         4.60        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.02         9.37         4.70        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         5.03         8.98         6.97        27.91         6.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.00         0.26       119.51        41.33        57.24       121.08 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
       24.13         0.49         2.40         2.17         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        0.66         6.90         7.10         3.98         2.73         5.23 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        2.76         2.04         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        47.70        47.08 

$`7P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-6672 
       19.53        10.62        13.55        19.10        12.72         7.33 
TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3887 
        2.01         0.99         1.02         0.95         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
        1.02         0.99         1.02         1.02        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A01Y 
        6.02        25.94        23.01        17.03        12.00        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       10.98        51.98        49.94        61.94        40.96         0.49 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 
        1.45         1.81         6.02         6.94        13.97         9.99 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DG TCGA-DY-A1H8 
        7.36        19.99         5.92         3.98        51.48        32.58 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 
        7.63         0.16         8.22         6.15         3.55         7.79 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6641 
        3.39         0.85         0.53         1.08        20.91 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.26              0.16 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           121.08             63.98 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             5.13              7.36 
[1] "0.3 - 121.1 (5.1)" "0.2 - 64.0 (7.4)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7P GAIN WILD-TYPE"   "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 WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-G5-6641 
"7P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7P GAIN WILD-TYPE"   "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 WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-G5-6641 
"7P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7P GAIN WILD-TYPE"   "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 WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-G5-6641 
"7P GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     42   48
  7P GAIN WILD-TYPE   32   40
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              42                32
  MALE                48                40
D13V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     87    2
  7P GAIN WILD-TYPE   56   11
                                clus
vv                               7P GAIN MUTATED 7P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       87                56
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    3 16 59 11
  7P GAIN WILD-TYPE  6 13 50  3
D13V5, multiclass
                   vv
clus                N0 N1 N2
  7P GAIN MUTATED   39 28 21
  7P GAIN WILD-TYPE 44 17 11
D13V6, multiclass
                   vv
clus                M0 M1 M1A MX
  7P GAIN MUTATED   65 14   1  8
  7P GAIN WILD-TYPE 58  8   1  5
D13V7, multiclass
                   vv
clus                 I II III IV
  7P GAIN MUTATED   15 23  31 16
  7P GAIN WILD-TYPE 15 27  19  9
D13V8, multiclass
D13V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3   87
  7P GAIN WILD-TYPE    3   69
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                3                 3
  YES              87                69

Clustering(14) Variable = 7q gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   56  6
  7Q GAIN WILD-TYPE 58  5
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               62                63 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                 5 
$`7Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       15.85        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3742 TCGA-AG-3878 
        6.35         1.02         1.02         1.02         0.99         0.99 
TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 
        0.99         1.02         1.02         1.02         0.99        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A02G 
       13.02         1.02         1.02        12.00        70.03        38.93 
TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
       38.01         0.69         0.72         4.60        10.19         6.02 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        9.37        60.00         7.99        10.98        11.01         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 
        8.98         6.97        27.91         6.97         5.00         0.26 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 
       41.33        57.24        24.13         0.49         2.17         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 
        3.98         0.66         6.90         7.10         3.98         2.76 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        2.17         0.39         1.02         0.69         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 
       47.70        47.08 

$`7Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        11.77        10.62        13.55        19.10        12.72 
TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        7.33         2.01         0.99         1.02         0.95         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-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A01Y 
        6.02        25.94        23.01        17.03        12.00        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       10.98        51.98        49.94         1.94        61.94        40.96 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.49         1.45         1.81         6.02         6.94         4.70 
TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97         9.99         7.36        19.99         5.92         3.98 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
      119.51       121.08        51.48        32.58         2.40         7.63 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
        0.16         8.22         6.15         3.55         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6814 
        7.79         2.04         3.39         0.85         0.66         0.53 
TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6641 
        1.08        18.25        20.91 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.26              0.16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            70.03            121.08 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            5.525             7.330 
[1] "0.3 - 70.0 (5.5)"  "0.2 - 121.1 (7.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7Q GAIN WILD-TYPE"   "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 WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-G5-6641 
"7Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7Q GAIN WILD-TYPE"   "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 WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-G5-6641 
"7Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7Q GAIN WILD-TYPE"   "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 WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-G5-6641 
"7Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     36   43
  7Q GAIN WILD-TYPE   38   45
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              36                38
  MALE                43                45
D14V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     77    1
  7Q GAIN WILD-TYPE   66   12
                                clus
vv                               7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       77                66
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    3 15 51  9
  7Q GAIN WILD-TYPE  6 14 58  5
D14V5, multiclass
                   vv
clus                N0 N1 N2
  7Q GAIN MUTATED   32 26 19
  7Q GAIN WILD-TYPE 51 19 13
D14V6, multiclass
                   vv
clus                M0 M1 M1A MX
  7Q GAIN MUTATED   55 13   1  8
  7Q GAIN WILD-TYPE 68  9   1  5
D14V7, multiclass
                   vv
clus                 I II III IV
  7Q GAIN MUTATED   14 16  31 14
  7Q GAIN WILD-TYPE 16 34  19 11
D14V8, multiclass
D14V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   76
  7Q GAIN WILD-TYPE    3   80
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                3                 3
  YES              76                80

Clustering(15) Variable = 8p gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   17  4
  8P GAIN WILD-TYPE 97  7
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               21               104 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                 7 
$`8P GAIN MUTATED`
TCGA-AF-6655 TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 
        6.35         1.02         0.92         1.02         0.99         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6623 
       12.00        63.98        38.01         0.69         0.72         9.37 
TCGA-CL-5918 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6883 
        7.99        41.33        57.24        24.13         8.22         3.98 
TCGA-F5-6465 TCGA-F5-6863 TCGA-G5-6572 
        3.39         0.76        47.08 

$`8P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 
        1.02         0.95         0.99         0.99         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3999 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-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        70.03        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.93        61.94        40.96         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-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.70        13.97        60.00        10.98        11.01         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98         7.36         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.92         3.98         5.00         0.26       119.51 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      121.08        51.48        32.58         0.49         2.40         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        0.16         2.17         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
        7.10         6.15         3.55         2.73         5.23         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        2.76         2.04         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         0.53         1.08         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6641 
       47.70        20.91 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.69              0.16 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            63.98            121.08 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            6.350             6.525 
[1] "0.7 - 64.0 (6.3)"  "0.2 - 121.1 (6.5)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P GAIN WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G5-6641 
"8P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P GAIN WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G5-6641 
"8P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P GAIN WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-G5-6641 
"8P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     13   14
  8P GAIN WILD-TYPE   61   74
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              13                61
  MALE                14                74
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     25    2
  8P GAIN WILD-TYPE  118   11
                                clus
vv                               8P GAIN MUTATED 8P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       25               118
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    1  3 20  2
  8P GAIN WILD-TYPE  8 26 89 12
D15V5, multiclass
                   vv
clus                N0 N1 N2
  8P GAIN MUTATED   14  5  6
  8P GAIN WILD-TYPE 69 40 26
D15V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  8P GAIN MUTATED    19   5   0   2
  8P GAIN WILD-TYPE 104  17   2  11
D15V7, multiclass
                   vv
clus                 I II III IV
  8P GAIN MUTATED    2 11   7  5
  8P GAIN WILD-TYPE 28 39  43 20
D15V8, multiclass
D15V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   27
  8P GAIN WILD-TYPE    6  129
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                0                 6
  YES              27               129

Clustering(16) Variable = 8q gain mutation analysis
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   44  9
  8Q GAIN WILD-TYPE 70  2
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               53                72 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                 2 
$`8Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 
       15.85        11.77        10.62        17.62        10.39         6.35 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-3999 
        1.02         1.02         1.02         1.02         0.92         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        1.02         1.02         0.99        17.03        15.91         1.02 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
        1.02        12.00        70.03        63.98        51.98         1.94 
TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 
       38.01         0.69         0.72         6.02         9.37         4.70 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 
       60.00         7.99         5.03         7.36         6.97         3.98 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        5.00        41.33        57.24        24.13        32.58         0.49 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 
        8.22         6.90         3.98         5.23         3.39         2.17 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        18.25        47.70        47.08        20.91 

$`8Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       19.53        13.55        19.10        12.72        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3727 
        7.59         7.33         1.02         2.01         0.99         0.95 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 
        0.99         0.99         1.02         0.99         0.99         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A015 
       20.94        13.91         6.02        25.94        23.01        13.02 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       12.00        10.98        49.94        38.93        61.94        40.96 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
        0.49         1.45         4.60         1.81        10.19         6.02 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
        6.94        13.97        10.98        11.01         9.99         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
        6.97        27.91        19.99         5.92         0.26       119.51 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      121.08        51.48         2.40         7.63         0.16         2.17 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        0.46         3.98         0.66         7.10         6.15         3.55 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 
        2.73         7.79         2.76         2.04         0.85         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 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.49              0.16 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            70.03            121.08 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            6.900             6.085 
[1] "0.5 - 70.0 (6.9)"  "0.2 - 121.1 (6.1)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G5-6641 
  "8Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G5-6641 
  "8Q GAIN MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "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-3581        TCGA-AG-3582 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-G5-6641 
  "8Q GAIN MUTATED" 
[1] "hr=" "3.8"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     33   39
  8Q GAIN WILD-TYPE   41   49
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              33                41
  MALE                39                49
D16V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     67    3
  8Q GAIN WILD-TYPE   76   10
                                clus
vv                               8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       67                76
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    3 11 50  7
  8Q GAIN WILD-TYPE  6 18 59  7
D16V5, multiclass
                   vv
clus                N0 N1 N2
  8Q GAIN MUTATED   32 20 18
  8Q GAIN WILD-TYPE 51 25 14
D16V6, multiclass
                   vv
clus                M0 M1 M1A MX
  8Q GAIN MUTATED   50 14   0  7
  8Q GAIN WILD-TYPE 73  8   2  6
D16V7, multiclass
                   vv
clus                 I II III IV
  8Q GAIN MUTATED    9 23  23 12
  8Q GAIN WILD-TYPE 21 27  27 13
D16V8, multiclass
D16V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   71
  8Q GAIN WILD-TYPE    5   85
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                1                 5
  YES              71                85

Clustering(17) Variable = 9p gain mutation analysis
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED   21  3
  9P GAIN WILD-TYPE 93  8
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               24               101 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                 8 
$`9P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3587 TCGA-AG-3726 
       15.85        11.77        10.39         6.35         1.02         1.02 
TCGA-AG-3878 TCGA-AG-4001 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A032 
        0.99         1.02        70.03        10.98        51.98        38.01 
TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-4745 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 
        0.69         0.72        10.98       121.08         2.40         3.98 
TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-G5-6233 
        2.73         2.04         0.39         0.69         1.08        18.25 

$`9P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       19.53        10.62        13.55        19.10        12.72        17.62 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 
       14.50         8.45         7.59         7.33         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3887 
        2.01         0.99         0.95         1.02         0.99         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-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       12.00        63.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       40.96         0.49         1.45         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-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.00         7.99        11.01         9.99         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        7.10         6.15         3.55         5.23         7.79         2.76 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
        3.39         0.85         2.17         1.02         0.66         0.53 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        47.70        47.08        20.91 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.39              0.16 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           121.08            119.51 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            3.355             6.940 
[1] "0.4 - 121.1 (3.4)" "0.2 - 119.5 (6.9)"
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"9P GAIN WILD-TYPE" 
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"9P GAIN WILD-TYPE" 
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "9P GAIN MUTATED"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "9P GAIN MUTATED" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G5-6641 
"9P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     17   18
  9P GAIN WILD-TYPE   57   70
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              17                57
  MALE                18                70
D17V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     31    3
  9P GAIN WILD-TYPE  112   10
                                clus
vv                               9P GAIN MUTATED 9P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       31               112
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    0  5 26  4
  9P GAIN WILD-TYPE  9 24 83 10
D17V5, multiclass
                   vv
clus                N0 N1 N2
  9P GAIN MUTATED   17  8  9
  9P GAIN WILD-TYPE 66 37 23
D17V6, multiclass
                   vv
clus                M0 M1 M1A MX
  9P GAIN MUTATED   30  4   0  1
  9P GAIN WILD-TYPE 93 18   2 12
D17V7, multiclass
                   vv
clus                 I II III IV
  9P GAIN MUTATED    4 13  11  3
  9P GAIN WILD-TYPE 26 37  39 22
D17V8, multiclass
D17V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      0   35
  9P GAIN WILD-TYPE    6  121
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                0                 6
  YES              35               121

Clustering(18) Variable = 9q gain mutation analysis
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    14   3
  9Q GAIN WILD-TYPE 100   8
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               17               108 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                 8 
$`9Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3878 TCGA-AG-A020 TCGA-AG-A023 
       15.85        10.39         6.35         0.99        10.98        51.98 
TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-4745 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 
       38.01         0.72        10.98       121.08         2.40         3.98 
TCGA-EI-6884 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-G5-6233 
        2.73         0.39         0.69         1.08        18.25 

$`9Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        11.77        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 
       17.62        14.50         8.45         7.59         7.33         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02         0.99         0.92         1.02         0.99         0.99 
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-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       63.98        49.94         1.94        38.93        61.94        40.96 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        0.49         1.45         0.69         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-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.00         7.99        11.01         9.99         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        7.10         6.15         3.55         5.23         7.79         2.76 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        2.04         3.39         0.85         2.17         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.53         0.76         0.46        47.70        47.08        20.91 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.39              0.16 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           121.08            119.51 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            6.350             6.525 
[1] "0.4 - 121.1 (6.3)" "0.2 - 119.5 (6.5)"
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"9Q GAIN WILD-TYPE" 
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"9Q GAIN WILD-TYPE" 
       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 WILD-TYPE" "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-3581        TCGA-AG-3582 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "9Q GAIN MUTATED"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6641 
"9Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     11   15
  9Q GAIN WILD-TYPE   63   73
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              11                63
  MALE                15                73
D18V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     23    2
  9Q GAIN WILD-TYPE  120   11
                                clus
vv                               9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       23               120
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    0  3 20  3
  9Q GAIN WILD-TYPE  9 26 89 11
D18V5, multiclass
                   vv
clus                N0 N1 N2
  9Q GAIN MUTATED   12  7  6
  9Q GAIN WILD-TYPE 71 38 26
D18V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  9Q GAIN MUTATED    21   4   0   1
  9Q GAIN WILD-TYPE 102  18   2  12
D18V7, multiclass
                   vv
clus                 I II III IV
  9Q GAIN MUTATED    2 10   9  2
  9Q GAIN WILD-TYPE 28 40  41 23
D18V8, multiclass
D18V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   26
  9Q GAIN WILD-TYPE    6  130
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                 6
  YES              26               130

Clustering(19) Variable = 10p gain mutation analysis
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     5   1
  10P GAIN WILD-TYPE 109  10
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                119 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 10 
$`10P GAIN MUTATED`
TCGA-AF-2689 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W TCGA-DC-4745 TCGA-DY-A1DF 
       15.85        15.91         1.02        70.03        10.98        24.13 

$`10P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        11.77        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 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        17.03        13.02         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-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01         9.99         5.03         8.98         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.91         6.97        19.99         5.92         3.98         5.00 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        0.26       119.51        41.33        57.24       121.08        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         7.63         0.16         2.17 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
        8.22         0.46         3.98         0.66         6.90         7.10 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
        6.15         3.55         3.98         2.73         5.23         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        2.76         2.04         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        47.70        47.08        20.91 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.02               0.16 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             70.03             121.08 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             15.88               6.02 
[1] "1.0 - 70.0 (15.9)" "0.2 - 121.1 (6.0)"
        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-3581 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10P GAIN WILD-TYPE" "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-3581 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10P GAIN WILD-TYPE" "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-3581 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5    3
  10P GAIN WILD-TYPE   69   85
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                5                 69
  MALE                  3                 85
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    0
  10P GAIN WILD-TYPE  135   13
                                clus
vv                               10P GAIN MUTATED 10P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         8                135
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED     0   1   7   0
  10P GAIN WILD-TYPE   9  28 102  14
D19V5, multiclass
                    vv
clus                 N0 N1 N2
  10P GAIN MUTATED    4  1  3
  10P GAIN WILD-TYPE 79 44 29
D19V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  10P GAIN MUTATED     6   2   0   0
  10P GAIN WILD-TYPE 117  20   2  13
D19V7, multiclass
                    vv
clus                  I II III IV
  10P GAIN MUTATED    1  3   2  1
  10P GAIN WILD-TYPE 29 47  48 24
D19V8, multiclass
D19V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    8
  10P GAIN WILD-TYPE    6  148
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 0                  6
  YES                8                148

Clustering(20) Variable = 10q gain mutation analysis
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     4   0
  10Q GAIN WILD-TYPE 110  11
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                121 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                 11 
$`10Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AG-3999 TCGA-AG-A01W TCGA-DC-4745 
       15.85         1.02        70.03        10.98 

$`10Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        11.77        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 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 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-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        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-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        11.01         9.99         5.03         8.98         7.36 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        6.97        27.91         6.97        19.99         5.92         3.98 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.00         0.26       119.51        41.33        57.24       121.08 
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         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        0.16         2.17         8.22         0.46         3.98         0.66 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        6.90         7.10         6.15         3.55         3.98         2.73 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
        5.23         7.79         2.76         2.04         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        47.70        47.08 
TCGA-G5-6641 
       20.91 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.02               0.16 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             70.03             121.08 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            13.415              6.150 
[1] "1.0 - 70.0 (13.4)" "0.2 - 121.1 (6.2)"
        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-3581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10Q GAIN WILD-TYPE" "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-3581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10Q GAIN WILD-TYPE" "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-3581 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10Q GAIN WILD-TYPE"   "10Q GAIN MUTATED" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
[1] "hr="     "7.7e+07"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4    0
  10Q GAIN WILD-TYPE   70   88
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  0                 88
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4    0
  10Q GAIN WILD-TYPE  139   13
                                clus
vv                               10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         4                139
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     0   0   4   0
  10Q GAIN WILD-TYPE   9  29 105  14
D20V5, multiclass
                    vv
clus                 N0 N1 N2
  10Q GAIN MUTATED    1  1  2
  10Q GAIN WILD-TYPE 82 44 30
D20V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  10Q GAIN MUTATED     3   1   0   0
  10Q GAIN WILD-TYPE 120  21   2  13
D20V7, multiclass
                    vv
clus                  I II III IV
  10Q GAIN MUTATED    0  1   2  0
  10Q GAIN WILD-TYPE 30 49  48 25
D20V8, multiclass
D20V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    4
  10Q GAIN WILD-TYPE    6  152
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 0                  6
  YES                4                152

Clustering(21) Variable = 11p gain mutation analysis
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    14   2
  11P GAIN WILD-TYPE 100   9
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                16                109 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  9 
$`11P GAIN MUTATED`
TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3587 TCGA-AG-4007 TCGA-AG-A01N TCGA-AH-6897 
       10.39         6.35         1.02         1.02        12.00         4.60 
TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 
        9.37        11.01         5.03         8.98        27.91        19.99 
TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6885 TCGA-G5-6233 
      119.51         2.40         5.23        18.25 

$`11P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       12.72        17.62        14.50         8.45         7.59         7.33 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         2.01         0.99         1.02         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-4001 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-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-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-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-5337 TCGA-DC-6155 
       13.97        60.00         7.99        10.98         9.99         7.36 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.97         6.97         5.92         3.98         5.00         0.26 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.33        57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        3.98         2.73         7.79         2.76         2.04         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-G5-6235 TCGA-G5-6572 
        0.53         1.08         0.76         0.46        47.70        47.08 
TCGA-G5-6641 
       20.91 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.02               0.16 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            119.51             121.08 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             9.175              6.020 
[1] "1.0 - 119.5 (9.2)" "0.2 - 121.1 (6.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        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-3581 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        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-3581 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        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-3581 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED"   "11P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7   14
  11P GAIN WILD-TYPE   67   74
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                7                 67
  MALE                 14                 74
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     21    0
  11P GAIN WILD-TYPE  122   13
                                clus
vv                               11P GAIN MUTATED 11P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        21                122
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    1  7 11  2
  11P GAIN WILD-TYPE  8 22 98 12
D21V5, multiclass
                    vv
clus                 N0 N1 N2
  11P GAIN MUTATED   12  5  4
  11P GAIN WILD-TYPE 71 40 28
D21V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  11P GAIN MUTATED    16   5   0   0
  11P GAIN WILD-TYPE 107  17   2  13
D21V7, multiclass
                    vv
clus                  I II III IV
  11P GAIN MUTATED    6  6   4  4
  11P GAIN WILD-TYPE 24 44  46 21
D21V8, multiclass
D21V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   21
  11P GAIN WILD-TYPE    6  135
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 0                  6
  YES               21                135

Clustering(22) Variable = 11q gain mutation analysis
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    12   1
  11Q GAIN WILD-TYPE 102  10
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                112 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 10 
$`11Q GAIN MUTATED`
TCGA-AF-3913 TCGA-AG-4007 TCGA-AG-A01N TCGA-AH-6897 TCGA-CI-6623 TCGA-CI-6624 
       10.39         1.02        12.00         4.60         9.37         4.70 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DY-A0XA TCGA-EI-6885 
       11.01         5.03         8.98        27.91       119.51         5.23 
TCGA-F5-6812 
        0.66 

$`11Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        17.62        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
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-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         9.99 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        7.36         6.97         6.97        19.99         5.92         3.98 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.00         0.26        41.33        57.24       121.08        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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
        7.10         6.15         3.55         3.98         2.73         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        2.76         2.04         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         0.69         0.53         1.08         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        47.70        47.08        20.91 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.66               0.16 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            119.51             121.08 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              8.98               6.25 
[1] "0.7 - 119.5 (9.0)" "0.2 - 121.1 (6.2)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        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-3581 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        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-3581 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        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-3581 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED"   "11Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      7   10
  11Q GAIN WILD-TYPE   67   78
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                7                 67
  MALE                 10                 78
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     17    0
  11Q GAIN WILD-TYPE  126   13
                                clus
vv                               11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        17                126
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED     1   6   8   2
  11Q GAIN WILD-TYPE   8  23 101  12
D22V5, multiclass
                    vv
clus                 N0 N1 N2
  11Q GAIN MUTATED   11  4  2
  11Q GAIN WILD-TYPE 72 41 30
D22V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  11Q GAIN MUTATED    12   5   0   0
  11Q GAIN WILD-TYPE 111  17   2  13
D22V7, multiclass
                    vv
clus                  I II III IV
  11Q GAIN MUTATED    6  4   2  4
  11Q GAIN WILD-TYPE 24 46  48 21
D22V8, multiclass
D22V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   17
  11Q GAIN WILD-TYPE    6  139
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  6
  YES               17                139

Clustering(23) Variable = 12p gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   16  3
  12P GAIN WILD-TYPE 98  8
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                19                106 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                  8 
$`12P GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3887 
       17.62         8.45         7.33         1.02         1.02         0.92 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-CL-5917 TCGA-DY-A0XA 
       15.91        13.02        38.93        61.94        60.00       119.51 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 
       32.58         0.16         0.46         0.66         5.23         2.76 
TCGA-G5-6233 
       18.25 

$`12P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 
       12.72        10.39        14.50         7.59         6.35         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        1.02         2.01         0.99         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 
        0.99         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-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       25.94        23.01        17.03         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-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        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-5918 TCGA-DC-4745 
        6.94         9.37         4.70        13.97         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01         9.99         5.03         8.98         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.91         6.97        19.99         5.92         3.98         5.00 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        0.26        41.33        57.24       121.08        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
        0.49         2.40         7.63         2.17         8.22         3.98 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        6.90         7.10         6.15         3.55         3.98         2.73 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        7.79         2.04         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-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        47.70        47.08        20.91 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.16               0.26 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            119.51             121.08 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             8.450              6.085 
[1] "0.2 - 119.5 (8.4)" "0.3 - 121.1 (6.1)"
        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 WILD-TYPE"   "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-3581 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12P GAIN WILD-TYPE" "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 WILD-TYPE"   "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-3581 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12P GAIN WILD-TYPE" "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 WILD-TYPE"   "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-3581 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13   15
  12P GAIN WILD-TYPE   61   73
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               13                 61
  MALE                 15                 73
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     25    2
  12P GAIN WILD-TYPE  118   11
                                clus
vv                               12P GAIN MUTATED 12P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        25                118
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    1  9 16  2
  12P GAIN WILD-TYPE  8 20 93 12
D23V5, multiclass
                    vv
clus                 N0 N1 N2
  12P GAIN MUTATED   16  5  7
  12P GAIN WILD-TYPE 67 40 25
D23V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  12P GAIN MUTATED    21   3   0   4
  12P GAIN WILD-TYPE 102  19   2   9
D23V7, multiclass
                    vv
clus                  I II III IV
  12P GAIN MUTATED    7  9   7  5
  12P GAIN WILD-TYPE 23 41  43 20
D23V8, multiclass
D23V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2   26
  12P GAIN WILD-TYPE    4  130
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 2                  4
  YES               26                130

Clustering(24) Variable = 12q gain mutation analysis
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     9   3
  12Q GAIN WILD-TYPE 105   8
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                12                113 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                  8 
$`12Q GAIN MUTATED`
TCGA-AF-5654 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-DY-A0XA TCGA-DY-A1H8 
        8.45        13.02        38.93        61.94       119.51        32.58 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-G5-6233 
        0.16         0.46         0.66         5.23         2.76        18.25 

$`12Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        17.03        15.91         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-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        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         9.99         5.03         8.98         7.36 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        6.97        27.91         6.97        19.99         5.92         3.98 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.00         0.26        41.33        57.24       121.08        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         7.63         2.17         8.22 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        3.98         6.90         7.10         6.15         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        2.73         7.79         2.04         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        47.70        47.08        20.91 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.16               0.26 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            119.51             121.08 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            10.735              6.150 
[1] "0.2 - 119.5 (10.7)" "0.3 - 121.1 (6.2)" 
        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 WILD-TYPE" "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-3581 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12Q GAIN WILD-TYPE" "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 WILD-TYPE" "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-3581 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12Q GAIN WILD-TYPE" "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 WILD-TYPE" "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-3581 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     11    8
  12Q GAIN WILD-TYPE   63   80
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               11                 63
  MALE                  8                 80
D24V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     17    1
  12Q GAIN WILD-TYPE  126   12
                                clus
vv                               12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        17                126
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    1  6 11  1
  12Q GAIN WILD-TYPE  8 23 98 13
D24V5, multiclass
                    vv
clus                 N0 N1 N2
  12Q GAIN MUTATED   11  5  3
  12Q GAIN WILD-TYPE 72 40 29
D24V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  12Q GAIN MUTATED    15   3   0   1
  12Q GAIN WILD-TYPE 108  19   2  12
D24V7, multiclass
                    vv
clus                  I II III IV
  12Q GAIN MUTATED    4  7   4  4
  12Q GAIN WILD-TYPE 26 43  46 21
D24V8, multiclass
D24V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   19
  12Q GAIN WILD-TYPE    6  137
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 0                  6
  YES               19                137

Clustering(25) Variable = 13q gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED   73 11
  13Q GAIN WILD-TYPE 41  0
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                84                 41 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                11                  0 
$`13Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       15.85        11.77        10.62        13.55        19.10        17.62 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 
       10.39        14.50         7.59         6.35         7.33         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3887 
        1.02         2.01         1.02         0.95         0.99         0.92 
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-A00C TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        0.99         6.02        25.94        15.91        13.02         1.02 
TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        63.98        51.98        49.94         1.94        38.93 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       38.01         0.49         0.69         0.72         4.60         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-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       10.98        11.01         5.03         8.98        27.91         6.97 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.00        41.33        57.24       121.08        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         7.63         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        0.66         6.90         7.10         6.15         3.98         2.73 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        2.76         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        47.70        47.08 

$`13Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3731 
       19.53        12.72         8.45         0.99         1.02         1.02 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 
        0.99         1.02        20.94        13.91        23.01        17.03 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X 
        1.02        12.00        70.03        10.98        61.94        40.96 
TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-6155 
        1.45         1.81        10.19         6.02         9.99         7.36 
TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
        6.97        19.99         5.92         3.98         0.26       119.51 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
        2.40         0.16         2.17         3.55         5.23         7.79 
TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6641 
        2.04         0.53         1.08         0.46        20.91 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.39               0.16 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            121.08             119.51 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             6.625              6.020 
[1] "0.4 - 121.1 (6.6)" "0.2 - 119.5 (6.0)"
        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-3581 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"13Q GAIN WILD-TYPE" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        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-3581 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"13Q GAIN WILD-TYPE" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        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-3581 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"13Q GAIN WILD-TYPE" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
[1] "hr="     "3.3e+08"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     46   56
  13Q GAIN WILD-TYPE   28   32
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               46                 28
  MALE                 56                 32
D25V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     96    2
  13Q GAIN WILD-TYPE   47   11
                                clus
vv                               13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        96                 47
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    5 16 68 12
  13Q GAIN WILD-TYPE  4 13 41  2
D25V5, multiclass
                    vv
clus                 N0 N1 N2
  13Q GAIN MUTATED   44 32 24
  13Q GAIN WILD-TYPE 39 13  8
D25V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  13Q GAIN MUTATED   76 15   0 10
  13Q GAIN WILD-TYPE 47  7   2  3
D25V7, multiclass
                    vv
clus                  I II III IV
  13Q GAIN MUTATED   17 27  37 15
  13Q GAIN WILD-TYPE 13 23  13 10
D25V8, multiclass
D25V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3   99
  13Q GAIN WILD-TYPE    3   57
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 3                  3
  YES               99                 57

Clustering(26) Variable = 14q gain mutation analysis
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     4   0
  14Q GAIN WILD-TYPE 110  11
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                121 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                 11 
$`14Q GAIN MUTATED`
TCGA-AF-6136 TCGA-AG-A01Y TCGA-EI-6512 TCGA-EI-6885 
        7.59        63.98         0.66         5.23 

$`14Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        12.00        70.03        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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98         7.36         6.97        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        3.98         6.90         7.10         6.15         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
        2.73         7.79         2.76         2.04         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        47.70        47.08 
TCGA-G5-6641 
       20.91 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.66               0.16 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             63.98             121.08 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              6.41               6.35 
[1] "0.7 - 64.0 (6.4)"  "0.2 - 121.1 (6.3)"
        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-3581 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"14Q GAIN WILD-TYPE" "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-3581 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"14Q GAIN WILD-TYPE" "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-3581 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr="     "7.7e+07"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    0
  14Q GAIN WILD-TYPE   70   88
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  0                 88
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    0
  14Q GAIN WILD-TYPE  139   13
                                clus
vv                               14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         4                139
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     0   0   4   0
  14Q GAIN WILD-TYPE   9  29 105  14
D26V5, multiclass
                    vv
clus                 N0 N1 N2
  14Q GAIN MUTATED    1  3  0
  14Q GAIN WILD-TYPE 82 42 32
D26V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  14Q GAIN MUTATED     2   1   0   1
  14Q GAIN WILD-TYPE 121  21   2  12
D26V7, multiclass
                    vv
clus                  I II III IV
  14Q GAIN MUTATED    0  1   2  1
  14Q GAIN WILD-TYPE 30 49  48 24
D26V8, multiclass
D26V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    3
  14Q GAIN WILD-TYPE    5  153
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 1                  5
  YES                3                153

Clustering(27) Variable = 16p gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   23  0
  16P GAIN WILD-TYPE 91 11
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                102 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                 11 
$`16P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3726 TCGA-AG-4022 
       15.85        17.62         7.59         6.35         1.02         0.99 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A032 TCGA-AH-6644 
       15.91        13.02         1.02        12.00        38.01         0.72 
TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6683 TCGA-EI-6512 
        6.94        60.00        11.01         8.98         5.00         0.66 
TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6863 
        7.10         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 
       19.53        11.77        10.62        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 
       10.39        14.50         8.45         7.33         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3587 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-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-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         1.02        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       25.94        23.01        17.03         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-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-6623 TCGA-CI-6624 
        1.81        10.19         6.02         6.02         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       13.97         7.99        10.98         9.99         5.03         7.36 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        6.97        27.91         6.97        19.99         5.92         3.98 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        0.26       119.51        41.33        57.24       121.08        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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
        2.17         8.22         0.46         3.98         6.90         6.15 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        3.55         3.98         2.73         5.23         7.79         2.76 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        2.04         0.85         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.08         0.46        18.25        47.70        47.08        20.91 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.39               0.16 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             60.00             121.08 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             6.940              6.085 
[1] "0.4 - 60.0 (6.9)"  "0.2 - 121.1 (6.1)"
        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-3581 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16P GAIN WILD-TYPE" "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-3581 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16P GAIN WILD-TYPE" "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-3581 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr="     "2.2e+08"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     15   14
  16P GAIN WILD-TYPE   59   74
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               15                 59
  MALE                 14                 74
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     29    0
  16P GAIN WILD-TYPE  114   13
                                clus
vv                               16P GAIN MUTATED 16P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        29                114
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    1  5 19  4
  16P GAIN WILD-TYPE  8 24 90 10
D27V5, multiclass
                    vv
clus                 N0 N1 N2
  16P GAIN MUTATED   12 10  6
  16P GAIN WILD-TYPE 71 35 26
D27V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  16P GAIN MUTATED    20   5   0   4
  16P GAIN WILD-TYPE 103  17   2   9
D27V7, multiclass
                    vv
clus                  I II III IV
  16P GAIN MUTATED    4  7  12  4
  16P GAIN WILD-TYPE 26 43  38 21
D27V8, multiclass
D27V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   27
  16P GAIN WILD-TYPE    4  129
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 2                  4
  YES               27                129

Clustering(28) Variable = 16q gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   23  2
  16Q GAIN WILD-TYPE 91  9
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                25                100 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                  9 
$`16Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-4022 
       15.85        17.62        10.39         7.59         6.35         0.99 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A032 TCGA-AH-6644 
       15.91        13.02         1.02        12.00        38.01         0.72 
TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DG TCGA-EI-6512 
       60.00        11.01         8.98         5.00        51.48         0.66 
TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
        7.10         3.39         2.17         0.39         0.66         0.69 
TCGA-F5-6863 
        0.76 

$`16Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        11.77        10.62        13.55        19.10        12.72 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       14.50         8.45         7.33         1.02         1.02         2.01 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        1.02         0.99         1.02         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-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         1.02        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       25.94        23.01        17.03         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-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-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
        4.70        13.97         7.99        10.98         9.99         5.03 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        3.98         0.26       119.51        41.33        57.24       121.08 
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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
        2.17         8.22         0.46         3.98         6.90         6.15 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        3.55         3.98         2.73         5.23         7.79         2.76 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        2.04         0.85         1.02         0.53         1.08         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.25        47.70        47.08        20.91 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.39               0.16 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             60.00             121.08 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             7.100              6.085 
[1] "0.4 - 60.0 (7.1)"  "0.2 - 121.1 (6.1)"
        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-3581 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16Q GAIN WILD-TYPE" "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-3581 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16Q GAIN WILD-TYPE" "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-3581 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     14   16
  16Q GAIN WILD-TYPE   60   72
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               14                 60
  MALE                 16                 72
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     30    0
  16Q GAIN WILD-TYPE  113   13
                                clus
vv                               16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        30                113
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    1  4 22  3
  16Q GAIN WILD-TYPE  8 25 87 11
D28V5, multiclass
                    vv
clus                 N0 N1 N2
  16Q GAIN MUTATED   11 11  7
  16Q GAIN WILD-TYPE 72 34 25
D28V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  16Q GAIN MUTATED    19   7   0   4
  16Q GAIN WILD-TYPE 104  15   2   9
D28V7, multiclass
                    vv
clus                  I II III IV
  16Q GAIN MUTATED    3  7  12  5
  16Q GAIN WILD-TYPE 27 43  38 20
D28V8, multiclass
D28V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   28
  16Q GAIN WILD-TYPE    4  128
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 2                  4
  YES               28                128

Clustering(29) Variable = 17p gain mutation analysis
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     2   0
  17P GAIN WILD-TYPE 112  11
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                123 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                 11 
$`17P GAIN MUTATED`
TCGA-CI-6623 TCGA-DC-6154 
        9.37         8.98 

$`17P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-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-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-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         9.99 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        5.03         7.36         6.97        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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 
       47.70        47.08        20.91 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              8.98               0.16 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              9.37             121.08 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             9.175              6.150 
[1] "9.0 - 9.4 (9.2)"   "0.2 - 121.1 (6.2)"
        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-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        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-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        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-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                123 
        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-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6624 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "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-6155         TCGA-DC-6156 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6514         TCGA-EI-6881         TCGA-EI-6882 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6883         TCGA-EI-6884         TCGA-EI-6885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6917         TCGA-EI-7002         TCGA-EI-7004 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6810         TCGA-F5-6811         TCGA-F5-6812 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6813         TCGA-F5-6814         TCGA-F5-6861 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6863         TCGA-F5-6864         TCGA-G5-6233 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6235         TCGA-G5-6572         TCGA-G5-6641 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    1
  17P GAIN WILD-TYPE   72   87
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 72
  MALE                  1                 87
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    0
  17P GAIN WILD-TYPE  140   13
                                clus
vv                               17P GAIN MUTATED 17P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         3                140
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED     1   0   1   1
  17P GAIN WILD-TYPE   8  29 108  13
D29V5, multiclass
                    vv
clus                 N0 N1 N2
  17P GAIN MUTATED    1  0  2
  17P GAIN WILD-TYPE 82 45 30
D29V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  17P GAIN MUTATED     2   1   0   0
  17P GAIN WILD-TYPE 121  21   2  13
D29V7, multiclass
                    vv
clus                  I II III IV
  17P GAIN MUTATED    1  0   1  1
  17P GAIN WILD-TYPE 29 50  49 24
D29V8, multiclass
D29V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    3
  17P GAIN WILD-TYPE    6  153
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  6
  YES                3                153

Clustering(30) Variable = 17q gain mutation analysis
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    13   0
  17Q GAIN WILD-TYPE 101  11
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                13                112 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                 11 
$`17Q GAIN MUTATED`
TCGA-AF-2690 TCGA-AG-3587 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6897 
       11.77         1.02        15.91         1.02        12.00         4.60 
TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-7002 
        8.98         3.98         5.00         8.22         7.10         2.76 
TCGA-F5-6811 
        1.02 

$`17Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        15.85        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 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3726 
        7.33         1.02         1.02         2.01         0.99         1.02 
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-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-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       17.03        13.02         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-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-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-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        9.99         5.03         7.36         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       19.99         5.92         0.26       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      121.08        24.13        51.48        32.58         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        7.63         0.16         2.17         0.46         3.98         0.66 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        6.90         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        7.79         2.04         3.39         0.85         2.17         0.39 
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        47.70        47.08        20.91 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.02               0.16 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             15.91             121.08 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             5.000              6.625 
[1] "1.0 - 15.9 (5.0)"  "0.2 - 121.1 (6.6)"
        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-3581 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        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-3581 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        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-3581 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
[1] "hr="     "2.9e+07"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7   11
  17Q GAIN WILD-TYPE   67   77
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                7                 67
  MALE                 11                 77
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     18    0
  17Q GAIN WILD-TYPE  125   13
                                clus
vv                               17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        18                125
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    0  4 12  2
  17Q GAIN WILD-TYPE  9 25 97 12
D30V5, multiclass
                    vv
clus                 N0 N1 N2
  17Q GAIN MUTATED   10  2  6
  17Q GAIN WILD-TYPE 73 43 26
D30V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  17Q GAIN MUTATED    14   4   0   0
  17Q GAIN WILD-TYPE 109  18   2  13
D30V7, multiclass
                    vv
clus                  I II III IV
  17Q GAIN MUTATED    3  6   4  4
  17Q GAIN WILD-TYPE 27 44  46 21
D30V8, multiclass
D30V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   18
  17Q GAIN WILD-TYPE    6  138
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  6
  YES               18                138

Clustering(31) Variable = 18p gain mutation analysis
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED     2   1
  18P GAIN WILD-TYPE 112  10
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                122 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 10 
$`18P GAIN MUTATED`
TCGA-AF-6672 TCGA-AG-A01Y TCGA-AG-A02G 
        7.33        63.98        38.93 

$`18P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        6.35         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        12.00        70.03        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         9.99         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      121.08        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 
        7.63         0.16         2.17         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        0.66         6.90         7.10         6.15         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        2.73         5.23         7.79         2.76         2.04         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              7.33               0.16 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             63.98             121.08 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            38.930              6.085 
[1] "7.3 - 64.0 (38.9)" "0.2 - 121.1 (6.1)"
        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-3581 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"18P GAIN WILD-TYPE" "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-3581 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"18P GAIN WILD-TYPE" "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-3581 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    4
  18P GAIN WILD-TYPE   71   84
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 71
  MALE                  4                 84
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    1
  18P GAIN WILD-TYPE  137   12
                                clus
vv                               18P GAIN MUTATED 18P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                137
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED     0   1   4   2
  18P GAIN WILD-TYPE   9  28 105  12
D31V5, multiclass
                    vv
clus                 N0 N1 N2
  18P GAIN MUTATED    2  2  3
  18P GAIN WILD-TYPE 81 43 29
D31V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  18P GAIN MUTATED     4   1   0   2
  18P GAIN WILD-TYPE 119  21   2  11
D31V7, multiclass
                    vv
clus                  I II III IV
  18P GAIN MUTATED    0  2   3  2
  18P GAIN WILD-TYPE 30 48  47 23
D31V8, multiclass
D31V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    6
  18P GAIN WILD-TYPE    5  150
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  5
  YES                6                150

Clustering(32) Variable = 18q gain mutation analysis
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     1   1
  18Q GAIN WILD-TYPE 113  10
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                123 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 10 
$`18Q GAIN MUTATED`
TCGA-AF-6672 TCGA-AG-A02G 
        7.33        38.93 

$`18Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        6.35         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       49.94         1.94        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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98         7.36         6.97        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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 
       47.70        47.08        20.91 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              7.33               0.16 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             38.93             121.08 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             23.13               6.15 
[1] "7.3 - 38.9 (23.1)" "0.2 - 121.1 (6.2)"
        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-3581 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"18Q GAIN WILD-TYPE" "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-3581 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"18Q GAIN WILD-TYPE" "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-3581 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                123 
        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-AG-3581         TCGA-AG-3582 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3583         TCGA-AG-3587         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3731 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3742         TCGA-AG-3878         TCGA-AG-3887 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"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-A02N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032         TCGA-AH-6544 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6643         TCGA-AH-6644 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6897         TCGA-AH-6903         TCGA-BM-6198 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6619         TCGA-CI-6620         TCGA-CI-6622 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6623         TCGA-CI-6624         TCGA-CL-4957 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-4745 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-4749         TCGA-DC-5337         TCGA-DC-5869 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6154         TCGA-DC-6155         TCGA-DC-6156 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6514         TCGA-EI-6881         TCGA-EI-6882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6883         TCGA-EI-6884         TCGA-EI-6885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6917         TCGA-EI-7002         TCGA-EI-7004 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6810         TCGA-F5-6811         TCGA-F5-6812 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6813         TCGA-F5-6814         TCGA-F5-6861 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6863         TCGA-F5-6864         TCGA-G5-6233 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6235         TCGA-G5-6572         TCGA-G5-6641 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    3
  18Q GAIN WILD-TYPE   73   85
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 73
  MALE                  3                 85
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE  139   13
                                clus
vv                               18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         4                139
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED     0   1   1   2
  18Q GAIN WILD-TYPE   9  28 108  12
D32V5, multiclass
                    vv
clus                 N0 N1 N2
  18Q GAIN MUTATED    0  2  2
  18Q GAIN WILD-TYPE 83 43 30
D32V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  18Q GAIN MUTATED     1   1   0   2
  18Q GAIN WILD-TYPE 122  21   2  11
D32V7, multiclass
                    vv
clus                  I II III IV
  18Q GAIN MUTATED    0  0   2  2
  18Q GAIN WILD-TYPE 30 50  48 23
D32V8, multiclass
D32V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    3
  18Q GAIN WILD-TYPE    5  153
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                  5
  YES                3                153

Clustering(33) Variable = 19p gain mutation analysis
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    14   1
  19P GAIN WILD-TYPE 100  10
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                15                110 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 10 
$`19P GAIN MUTATED`
TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A01N 
       11.77         1.02         1.02         1.02        15.91        12.00 
TCGA-AG-A026 TCGA-AG-A032 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 TCGA-DY-A1DE 
        1.94        38.01        10.98        11.01         8.98       121.08 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 
        0.66         7.10         5.23 

$`19P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       19.53        15.85        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 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        7.33         1.02         2.01         0.99         1.02         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-4001 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-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       13.91         6.02        25.94        23.01        17.03        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02         1.02        12.00        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-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-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       60.00         7.99         9.99         5.03         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.91         6.97        19.99         5.92         3.98         5.00 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        0.26       119.51        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         7.63         0.16         2.17 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
        8.22         0.46         3.98         6.90         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        3.98         2.73         7.79         2.76         2.04         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.66               0.16 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            121.08             119.51 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             8.980              6.085 
[1] "0.7 - 121.1 (9.0)" "0.2 - 119.5 (6.1)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "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-3581 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3599         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 WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "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-3581 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3599         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 WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "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-3581 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-3599         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 WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED"   "19P GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     11    9
  19P GAIN WILD-TYPE   63   79
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               11                 63
  MALE                  9                 79
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     20    0
  19P GAIN WILD-TYPE  123   13
                                clus
vv                               19P GAIN MUTATED 19P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        20                123
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    0  6 11  3
  19P GAIN WILD-TYPE  9 23 98 11
D33V5, multiclass
                    vv
clus                 N0 N1 N2
  19P GAIN MUTATED   10  5  5
  19P GAIN WILD-TYPE 73 40 27
D33V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  19P GAIN MUTATED    15   5   0   0
  19P GAIN WILD-TYPE 108  17   2  13
D33V7, multiclass
                    vv
clus                  I II III IV
  19P GAIN MUTATED    5  4   5  5
  19P GAIN WILD-TYPE 25 46  45 20
D33V8, multiclass
D33V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   20
  19P GAIN WILD-TYPE    6  136
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 0                  6
  YES               20                136

Clustering(34) Variable = 19q gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   16  1
  19Q GAIN WILD-TYPE 98 10
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                108 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 10 
$`19Q GAIN MUTATED`
TCGA-AG-3587 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N 
        1.02         1.02        15.91        13.02         1.02        12.00 
TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 
        1.94        38.01         6.02        13.97        10.98        11.01 
TCGA-DC-6154 TCGA-DY-A1DE TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 
        8.98       121.08         0.66         7.10         5.23 

$`19Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3599 
        6.35         7.33         1.02         1.02         2.01         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
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-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-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       17.03         1.02        12.00        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-5917 TCGA-CL-5918 
        6.02         6.94         9.37         4.70        60.00         7.99 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        9.99         5.03         7.36         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.92         3.98         5.00         0.26       119.51 
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-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        3.98         6.90         6.15         3.55         3.98         2.73 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        7.79         2.76         2.04         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        47.70        47.08        20.91 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.66               0.16 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            121.08             119.51 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             8.980              6.085 
[1] "0.7 - 121.1 (9.0)" "0.2 - 119.5 (6.1)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "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-3581 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3599         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 WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "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-3581 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3599         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 WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "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-3581 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-3599         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 WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED"   "19Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13   10
  19Q GAIN WILD-TYPE   61   78
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               13                 61
  MALE                 10                 78
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     23    0
  19Q GAIN WILD-TYPE  120   13
                                clus
vv                               19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        23                120
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED    1  6 12  4
  19Q GAIN WILD-TYPE  8 23 97 10
D34V5, multiclass
                    vv
clus                 N0 N1 N2
  19Q GAIN MUTATED   12  7  4
  19Q GAIN WILD-TYPE 71 38 28
D34V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  19Q GAIN MUTATED    17   6   0   0
  19Q GAIN WILD-TYPE 106  16   2  13
D34V7, multiclass
                    vv
clus                  I II III IV
  19Q GAIN MUTATED    6  5   6  6
  19Q GAIN WILD-TYPE 24 45  44 19
D34V8, multiclass
D34V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0   23
  19Q GAIN WILD-TYPE    6  133
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 0                  6
  YES               23                133

Clustering(35) Variable = 20p gain mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   70  5
  20P GAIN WILD-TYPE 44  6
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                75                 50 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                  6 
$`20P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       19.53        15.85        11.77        19.10        17.62        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 
        8.45         6.35         7.33         1.02         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        0.99         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C 
        0.99         1.02         1.02         1.02         1.02         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 
       25.94        23.01        17.03        13.02         1.02        51.98 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       40.96        38.01         0.49         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 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-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98         9.99         5.03         8.98         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE 
       27.91         6.97        19.99         5.92       119.51       121.08 
TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       24.13         2.40         7.63         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 
        3.98         0.66         7.10         3.98         5.23         2.76 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-F5-6863 
        3.39         0.39         1.02         0.66         1.08         0.76 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.25        47.70        47.08 

$`20P GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3583 
       10.62        13.55        12.72        14.50         7.59         2.01 
TCGA-AG-3726 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         0.99         0.99        20.94        13.91 
TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.91         1.02        12.00        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 
       10.98        49.94         1.94        38.93        61.94         1.45 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6682 
       10.19         6.02        60.00         7.99        11.01         3.98 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.00         0.26        41.33        57.24        51.48        32.58 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
        0.49         0.16         6.90         6.15         3.55         2.73 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 
        7.79         2.04         0.85         2.17         0.69         0.53 
TCGA-F5-6864 TCGA-G5-6641 
        0.46        20.91 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.39               0.16 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            121.08              70.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              6.02               7.69 
[1] "0.4 - 121.1 (6.0)" "0.2 - 70.0 (7.7)" 
        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-3581 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
  "20P GAIN MUTATED" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "20P GAIN MUTATED" "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-3581 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
  "20P GAIN MUTATED" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "20P GAIN MUTATED" "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-3581 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
  "20P GAIN MUTATED" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     39   56
  20P GAIN WILD-TYPE   35   32
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               39                 35
  MALE                 56                 32
D35V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     90    2
  20P GAIN WILD-TYPE   53   11
                                clus
vv                               20P GAIN MUTATED 20P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        90                 53
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    5 18 63  8
  20P GAIN WILD-TYPE  4 11 46  6
D35V5, multiclass
                    vv
clus                 N0 N1 N2
  20P GAIN MUTATED   46 24 23
  20P GAIN WILD-TYPE 37 21  9
D35V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  20P GAIN MUTATED   71 14   2  7
  20P GAIN WILD-TYPE 52  8   0  6
D35V7, multiclass
                    vv
clus                  I II III IV
  20P GAIN MUTATED   20 25  29 15
  20P GAIN WILD-TYPE 10 25  21 10
D35V8, multiclass
D35V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   92
  20P GAIN WILD-TYPE    3   64
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 3                  3
  YES               92                 64

Clustering(36) Variable = 20q gain mutation analysis
D36V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   94 11
  20Q GAIN WILD-TYPE 20  0
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               105                 20 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                11                  0 
$`20Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       19.53        15.85        11.77        10.62        19.10        17.62 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45         7.59         6.35         7.33 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        1.02         1.02         2.01         1.02         0.99         1.02 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3893 
        0.95         1.02         0.99         0.99         0.92         0.99 
TCGA-AG-3894 TCGA-AG-3999 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-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-A020 
        1.02         1.02        12.00        12.00        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98         1.94        38.93        40.96        38.01         0.49 
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-5918 TCGA-DC-4745 
        6.94         9.37         4.70        13.97         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01         9.99         5.03         8.98         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA 
       27.91         6.97        19.99         5.92         5.00       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.33        57.24       121.08        24.13        51.48        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40         7.63         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
        3.98         0.66         6.90         7.10         3.98         2.73 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        5.23         2.76         3.39         0.85         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         0.66         0.69         1.08         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.25        47.70        47.08 

$`20Q GAIN WILD-TYPE`
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01Y 
       13.55        12.72         1.02        20.94        13.91        63.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-BM-6198 TCGA-CL-5917 TCGA-DC-6682 
       49.94        61.94         1.45        10.19        60.00         3.98 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        0.26         0.16         6.15         3.55         7.79         2.04 
TCGA-F5-6814 TCGA-G5-6641 
        0.53        20.91 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.39               0.16 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            121.08              63.98 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              6.02               8.99 
[1] "0.4 - 121.1 (6.0)" "0.2 - 64.0 (9.0)" 
        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-3581 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        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-3581 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        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-3581 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
[1] "hr="     "3.2e+08"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     59   73
  20Q GAIN WILD-TYPE   15   15
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               59                 15
  MALE                 73                 15
D36V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    124    4
  20Q GAIN WILD-TYPE   19    9
                                clus
vv                               20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       124                 19
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    6 25 87 13
  20Q GAIN WILD-TYPE  3  4 22  1
D36V5, multiclass
                    vv
clus                 N0 N1 N2
  20Q GAIN MUTATED   63 40 27
  20Q GAIN WILD-TYPE 20  5  5
D36V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  20Q GAIN MUTATED   98 21   2 10
  20Q GAIN WILD-TYPE 25  1   0  3
D36V7, multiclass
                    vv
clus                  I II III IV
  20Q GAIN MUTATED   25 36  42 23
  20Q GAIN WILD-TYPE  5 14   8  2
D36V8, multiclass
D36V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4  128
  20Q GAIN WILD-TYPE    2   28
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 4                  2
  YES              128                 28

Clustering(37) Variable = 21q gain mutation analysis
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED     3   0
  21Q GAIN WILD-TYPE 111  11
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                122 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                 11 
$`21Q GAIN MUTATED`
TCGA-AG-A011 TCGA-AH-6644 TCGA-EI-6885 
       17.03         0.72         5.23 

$`21Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.94        23.01        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-6897 TCGA-AH-6903 TCGA-BM-6198 
        0.49         1.45         0.69         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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98         7.36         6.97        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        3.98         2.73         7.79         2.76         2.04         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.72               0.16 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             17.03             121.08 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             5.230              6.625 
[1] "0.7 - 17.0 (5.2)"  "0.2 - 121.1 (6.6)"
        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-3581 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"21Q GAIN WILD-TYPE" "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-3581 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"21Q GAIN WILD-TYPE" "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-3581 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr="     "3400000"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    3
  21Q GAIN WILD-TYPE   70   85
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  3                 85
D37V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    0
  21Q GAIN WILD-TYPE  136   13
                                clus
vv                               21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         7                136
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED     0   1   6   0
  21Q GAIN WILD-TYPE   9  28 103  14
D37V5, multiclass
                    vv
clus                 N0 N1 N2
  21Q GAIN MUTATED    3  2  1
  21Q GAIN WILD-TYPE 80 43 31
D37V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  21Q GAIN MUTATED     4   2   0   1
  21Q GAIN WILD-TYPE 119  20   2  12
D37V7, multiclass
                    vv
clus                  I II III IV
  21Q GAIN MUTATED    1  2   1  2
  21Q GAIN WILD-TYPE 29 48  49 23
D37V8, multiclass
D37V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    7
  21Q GAIN WILD-TYPE    6  149
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  6
  YES                7                149

Clustering(38) Variable = 22q gain mutation analysis
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     2   1
  22Q GAIN WILD-TYPE 112  10
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                122 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 10 
$`22Q GAIN MUTATED`
TCGA-AG-3582 TCGA-AH-6897 TCGA-DY-A1DF 
        1.02         4.60        24.13 

$`22Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        6.35         7.33         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-6903 TCGA-BM-6198 
        0.49         1.45         0.69         0.72         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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98         7.36         6.97        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       121.08        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 
        7.63         0.16         2.17         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        0.66         6.90         7.10         6.15         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        2.73         5.23         7.79         2.76         2.04         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.02               0.16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             24.13             121.08 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             4.600              6.625 
[1] "1.0 - 24.1 (4.6)"  "0.2 - 121.1 (6.6)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        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-3581 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        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-3581 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        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-3581 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr=" "10" 
D38V2, continuous
D38V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    2
  22Q GAIN WILD-TYPE   71   86
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 71
  MALE                  2                 86
D38V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    0
  22Q GAIN WILD-TYPE  138   13
                                clus
vv                               22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         5                138
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED     0   1   4   0
  22Q GAIN WILD-TYPE   9  28 105  14
D38V5, multiclass
                    vv
clus                 N0 N1 N2
  22Q GAIN MUTATED    1  2  2
  22Q GAIN WILD-TYPE 82 43 30
D38V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  22Q GAIN MUTATED     4   1   0   0
  22Q GAIN WILD-TYPE 119  21   2  13
D38V7, multiclass
                    vv
clus                  I II III IV
  22Q GAIN MUTATED    1  0   3  1
  22Q GAIN WILD-TYPE 29 50  47 24
D38V8, multiclass
D38V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    5
  22Q GAIN WILD-TYPE    6  151
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  6
  YES                5                151

Clustering(39) Variable = Xq gain mutation analysis
D39V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     6   0
  XQ GAIN WILD-TYPE 108  11
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                6               119 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                11 
$`XQ GAIN MUTATED`
TCGA-AG-4007 TCGA-AG-A015 TCGA-AG-A016 TCGA-CI-6623 TCGA-EI-6510 TCGA-F5-6465 
        1.02        13.02         1.02         9.37         0.46         3.39 

$`XQ GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 
        0.92         1.02         0.99         0.99         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-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        17.03        15.91         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-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         9.99         5.03         8.98         7.36 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        6.97        27.91         6.97        19.99         5.92         3.98 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.00         0.26       119.51        41.33        57.24       121.08 
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         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        0.16         2.17         8.22         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        7.79         2.76         2.04         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        47.70        47.08        20.91 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.46              0.16 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            13.02            121.08 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            2.205             6.900 
[1] "0.5 - 13.0 (2.2)"  "0.2 - 121.1 (6.9)"
       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 WILD-TYPE" "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 WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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 WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "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 WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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 WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "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 WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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 WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
  "XQ GAIN MUTATED"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6641 
"XQ GAIN WILD-TYPE" 
[1] "hr="     "3400000"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3    4
  XQ GAIN WILD-TYPE   71   84
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               3                71
  MALE                 4                84
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6    1
  XQ GAIN WILD-TYPE  137   12
                                clus
vv                               XQ GAIN MUTATED XQ GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        6               137
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED     2   1   3   1
  XQ GAIN WILD-TYPE   7  28 106  13
D39V5, multiclass
                   vv
clus                N0 N1 N2
  XQ GAIN MUTATED    5  0  2
  XQ GAIN WILD-TYPE 78 45 30
D39V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  XQ GAIN MUTATED     4   2   0   1
  XQ GAIN WILD-TYPE 119  20   2  12
D39V7, multiclass
                   vv
clus                 I II III IV
  XQ GAIN MUTATED    2  2   0  3
  XQ GAIN WILD-TYPE 28 48  50 22
D39V8, multiclass
D39V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    7
  XQ GAIN WILD-TYPE    6  149
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 6
  YES               7               149

Clustering(40) Variable = 1p loss mutation analysis
D40V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    12   2
  1P LOSS WILD-TYPE 102   9
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               14               111 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                 9 
$`1P LOSS MUTATED`
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A02G TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 
       23.01        12.00        38.93         0.69        10.19         9.37 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6160 TCGA-DY-A0XA TCGA-EI-6511 TCGA-EI-7002 
       11.01         5.03        19.99       119.51         3.98         2.76 
TCGA-F5-6811 TCGA-G5-6572 
        1.02        47.08 

$`1P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-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-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-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        4.70        13.97        60.00         7.99        10.98         9.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 
        8.98         7.36         6.97        27.91         6.97         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        3.98         5.00         0.26        41.33        57.24       121.08 
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         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
        0.16         2.17         8.22         0.46         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        7.79         2.04         3.39         0.85         2.17         0.39 
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-G5-6641 
       18.25        47.70        20.91 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.69              0.16 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           119.51            121.08 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            10.60              6.02 
[1] "0.7 - 119.5 (10.6)" "0.2 - 121.1 (6.0)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "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 WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G5-6641 
"1P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "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 WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G5-6641 
"1P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "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 WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G5-6641 
"1P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6   15
  1P LOSS WILD-TYPE   68   73
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               6                68
  MALE                15                73
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     20    0
  1P LOSS WILD-TYPE  123   13
                                clus
vv                               1P LOSS MUTATED 1P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       20               123
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    1  5 14  0
  1P LOSS WILD-TYPE  8 24 95 14
D40V5, multiclass
                   vv
clus                N0 N1 N2
  1P LOSS MUTATED    9  8  3
  1P LOSS WILD-TYPE 74 37 29
D40V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  1P LOSS MUTATED    15   3   0   1
  1P LOSS WILD-TYPE 108  19   2  12
D40V7, multiclass
                   vv
clus                 I II III IV
  1P LOSS MUTATED    5  4   8  3
  1P LOSS WILD-TYPE 25 46  42 22
D40V8, multiclass
D40V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1   20
  1P LOSS WILD-TYPE    5  136
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                1                 5
  YES              20               136

Clustering(41) Variable = 1q loss mutation analysis
D41V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED     4   0
  1Q LOSS WILD-TYPE 110  11
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               121 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                11 
$`1Q LOSS MUTATED`
TCGA-AG-A01L TCGA-BM-6198 TCGA-DC-5869 TCGA-EI-6511 
       12.00        10.19         5.03         3.98 

$`1Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-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-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        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-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-6154 
       60.00         7.99        10.98        11.01         9.99         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      121.08        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-6512 
        7.63         0.16         2.17         8.22         0.46         0.66 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        6.90         7.10         6.15         3.55         3.98         2.73 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
        5.23         7.79         2.76         2.04         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        47.70        47.08 
TCGA-G5-6641 
       20.91 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             3.98              0.16 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            12.00            121.08 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             7.61              6.35 
[1] "4.0 - 12.0 (7.6)"  "0.2 - 121.1 (6.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1Q LOSS WILD-TYPE" "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 WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"1Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1Q LOSS WILD-TYPE" "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 WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"1Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"1Q LOSS WILD-TYPE" "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 WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"1Q LOSS WILD-TYPE" 
[1] "hr="     "9500000"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    5
  1Q LOSS WILD-TYPE   72   83
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                72
  MALE                 5                83
D41V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7    0
  1Q LOSS WILD-TYPE  136   13
                                clus
vv                               1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        7               136
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED     0   1   6   0
  1Q LOSS WILD-TYPE   9  28 103  14
D41V5, multiclass
                   vv
clus                N0 N1 N2
  1Q LOSS MUTATED    1  5  1
  1Q LOSS WILD-TYPE 82 40 31
D41V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  1Q LOSS MUTATED     5   1   0   0
  1Q LOSS WILD-TYPE 118  21   2  13
D41V7, multiclass
                   vv
clus                 I II III IV
  1Q LOSS MUTATED    1  0   5  1
  1Q LOSS WILD-TYPE 29 50  45 24
D41V8, multiclass
D41V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    6
  1Q LOSS WILD-TYPE    5  150
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                1                 5
  YES               6               150

Clustering(42) Variable = 2p loss mutation analysis
D42V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     3   0
  2P LOSS WILD-TYPE 111  11
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3               122 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                11 
$`2P LOSS MUTATED`
TCGA-AG-3582 TCGA-AG-3999 TCGA-AG-A02X 
        1.02         1.02        40.96 

$`2P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        6.35         7.33         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 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-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-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.93        61.94        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         9.99         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      121.08        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 
        7.63         0.16         2.17         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        0.66         6.90         7.10         6.15         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        2.73         5.23         7.79         2.76         2.04         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.02              0.16 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            40.96            121.08 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            1.020             6.625 
[1] "1.0 - 41.0 (1.0)"  "0.2 - 121.1 (6.6)"
       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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"2P LOSS WILD-TYPE" 
[1] "hr="     "2.6e+07"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    2
  2P LOSS WILD-TYPE   71   86
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               3                71
  MALE                 2                86
D42V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    1
  2P LOSS WILD-TYPE  140   12
                                clus
vv                               2P LOSS MUTATED 2P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        3               140
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     0   1   4   0
  2P LOSS WILD-TYPE   9  28 105  14
D42V5, multiclass
                   vv
clus                N0 N1 N2
  2P LOSS MUTATED    3  1  1
  2P LOSS WILD-TYPE 80 44 31
D42V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  2P LOSS MUTATED     4   1   0   0
  2P LOSS WILD-TYPE 119  21   2  13
D42V7, multiclass
                   vv
clus                 I II III IV
  2P LOSS MUTATED    1  2   1  1
  2P LOSS WILD-TYPE 29 48  49 24
D42V8, multiclass
D42V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    5
  2P LOSS WILD-TYPE    6  151
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                0                 6
  YES               5               151

Clustering(43) Variable = 3p loss mutation analysis
D43V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     5   0
  3P LOSS WILD-TYPE 109  11
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5               120 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                11 
$`3P LOSS MUTATED`
TCGA-AG-3583 TCGA-AH-6544 TCGA-BM-6198 TCGA-DC-6682 TCGA-DT-5265 
        2.01         0.49        10.19         3.98         0.26 

$`3P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3599 
        6.35         7.33         1.02         1.02         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        1.45         0.69         0.72         4.60         1.81         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         9.99         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.00       119.51        41.33        57.24       121.08        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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        7.79         2.76         2.04         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        47.70        47.08        20.91 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.26              0.16 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            10.19            121.08 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             2.01              6.92 
[1] "0.3 - 10.2 (2.0)"  "0.2 - 121.1 (6.9)"
       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 WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"3P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"3P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"3P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"3P LOSS WILD-TYPE" 
[1] "hr="     "3500000"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2    6
  3P LOSS WILD-TYPE   72   82
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               2                72
  MALE                 6                82
D43V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    2
  3P LOSS WILD-TYPE  138   11
                                clus
vv                               3P LOSS MUTATED 3P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               138
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED     0   0   8   0
  3P LOSS WILD-TYPE   9  29 101  14
D43V5, multiclass
                   vv
clus                N0 N1 N2
  3P LOSS MUTATED    3  3  2
  3P LOSS WILD-TYPE 80 42 30
D43V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  3P LOSS MUTATED     4   3   0   0
  3P LOSS WILD-TYPE 119  19   2  13
D43V7, multiclass
                   vv
clus                 I II III IV
  3P LOSS MUTATED    0  3   2  2
  3P LOSS WILD-TYPE 30 47  48 23
D43V8, multiclass
D43V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    7
  3P LOSS WILD-TYPE    5  149
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                1                 5
  YES               7               149

Clustering(44) Variable = 3q loss mutation analysis
D44V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     3   0
  3Q LOSS WILD-TYPE 111  11
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3               122 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                11 
$`3Q LOSS MUTATED`
TCGA-AG-3583 TCGA-BM-6198 TCGA-DT-5265 
        2.01        10.19         0.26 

$`3Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3599 
        6.35         7.33         1.02         1.02         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98         7.36         6.97        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.92         3.98         5.00       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      121.08        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 
        7.63         0.16         2.17         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        0.66         6.90         7.10         6.15         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        2.73         5.23         7.79         2.76         2.04         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.26              0.16 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            10.19            121.08 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            2.010             6.625 
[1] "0.3 - 10.2 (2.0)"  "0.2 - 121.1 (6.6)"
       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 WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"3Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"3Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"3Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"3Q LOSS WILD-TYPE" 
[1] "hr="     "3400000"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    3
  3Q LOSS WILD-TYPE   73   85
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               1                73
  MALE                 3                85
D44V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    3
  3Q LOSS WILD-TYPE  142   10
                                clus
vv                               3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        1               142
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     0   0   4   0
  3Q LOSS WILD-TYPE   9  29 105  14
D44V5, multiclass
                   vv
clus                N0 N1 N2
  3Q LOSS MUTATED    2  1  1
  3Q LOSS WILD-TYPE 81 44 31
D44V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  3Q LOSS MUTATED     2   1   0   0
  3Q LOSS WILD-TYPE 121  21   2  13
D44V7, multiclass
                   vv
clus                 I II III IV
  3Q LOSS MUTATED    0  2   1  1
  3Q LOSS WILD-TYPE 30 48  49 24
D44V8, multiclass
D44V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1    3
  3Q LOSS WILD-TYPE    5  153
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                1                 5
  YES               3               153

Clustering(45) Variable = 4p loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   25  1
  4P LOSS WILD-TYPE 89 10
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               26                99 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                10 
$`4P LOSS MUTATED`
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3999 TCGA-AG-A008 
       17.62        14.50         7.59         1.02         1.02        13.91 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02X TCGA-AH-6643 
       25.94        23.01        12.00        70.03        40.96         0.69 
TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DE 
       10.19         6.02         6.97         6.97        19.99       121.08 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 
       32.58         2.40         6.90         6.15         2.76         0.85 
TCGA-F5-6702 TCGA-F5-6813 
        2.17         0.69 

$`4P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 
       12.72        10.39         8.45         6.35         7.33         1.02 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        2.01         1.02         0.99         1.02         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-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-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       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-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       61.94        38.01         0.49         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
        8.98         7.36        27.91         5.92         3.98         5.00 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        0.26       119.51        41.33        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        3.98         0.66         7.10         3.55         3.98         2.73 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
        5.23         7.79         2.04         3.39         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.53         1.08         0.76         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       47.70        47.08        20.91 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.69              0.16 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           121.08            119.51 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             7.28              5.92 
[1] "0.7 - 121.1 (7.3)" "0.2 - 119.5 (5.9)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "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-3581        TCGA-AG-3582 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"4P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "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-3581        TCGA-AG-3582 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"4P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "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-3581        TCGA-AG-3582 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"4P LOSS WILD-TYPE" 
[1] "hr=" "3"  
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     16   23
  4P LOSS WILD-TYPE   58   65
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              16                58
  MALE                23                65
D45V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     36    1
  4P LOSS WILD-TYPE  107   12
                                clus
vv                               4P LOSS MUTATED 4P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       36               107
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    0  7 29  3
  4P LOSS WILD-TYPE  9 22 80 11
D45V5, multiclass
                   vv
clus                N0 N1 N2
  4P LOSS MUTATED   17 12 10
  4P LOSS WILD-TYPE 66 33 22
D45V6, multiclass
                   vv
clus                M0 M1 M1A MX
  4P LOSS MUTATED   29  5   1  3
  4P LOSS WILD-TYPE 94 17   1 10
D45V7, multiclass
                   vv
clus                 I II III IV
  4P LOSS MUTATED    6 11  15  7
  4P LOSS WILD-TYPE 24 39  35 18
D45V8, multiclass
D45V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3   36
  4P LOSS WILD-TYPE    3  120
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                3                 3
  YES              36               120

Clustering(46) Variable = 4q loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   32  1
  4Q LOSS WILD-TYPE 82 10
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               33                92 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                10 
$`4Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 
       13.55        19.10        17.62        14.50         7.59         1.02 
TCGA-AG-3999 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-6643 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-4749 
       63.98        40.96         0.69        10.19         6.02        11.01 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
        6.97         6.97        19.99       121.08        32.58         2.40 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
        8.22         6.90         6.15         2.76         0.85         2.17 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        1.02         0.66         0.69 

$`4Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 
       19.53        15.85        11.77        10.62        12.72        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 
        8.45         6.35         7.33         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4007 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 
        1.02         0.99        20.94         6.02        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 
       13.02         1.02         1.02        12.00        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-6619 TCGA-CI-6622 
        1.45         0.72         4.60         1.81         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-6157 TCGA-DC-6681 
        9.99         5.03         8.98         7.36        27.91         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        41.33        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48         0.49         7.63         0.16         2.17 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
        0.46         3.98         0.66         7.10         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6810 
        2.73         5.23         7.79         2.04         3.39         0.39 
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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.66              0.16 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           121.08            119.51 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             8.22              5.13 
[1] "0.7 - 121.1 (8.2)" "0.2 - 119.5 (5.1)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "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-3581        TCGA-AG-3582 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"4Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "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-3581        TCGA-AG-3582 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"4Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "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-3581        TCGA-AG-3582 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"4Q LOSS WILD-TYPE" 
[1] "hr=" "4.6"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     18   28
  4Q LOSS WILD-TYPE   56   60
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              18                56
  MALE                28                60
D46V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     41    1
  4Q LOSS WILD-TYPE  102   12
                                clus
vv                               4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       41               102
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    0  9 33  4
  4Q LOSS WILD-TYPE  9 20 76 10
D46V5, multiclass
                   vv
clus                N0 N1 N2
  4Q LOSS MUTATED   22 13 11
  4Q LOSS WILD-TYPE 61 32 21
D46V6, multiclass
                   vv
clus                M0 M1 M1A MX
  4Q LOSS MUTATED   35  5   1  4
  4Q LOSS WILD-TYPE 88 17   1  9
D46V7, multiclass
                   vv
clus                 I II III IV
  4Q LOSS MUTATED    8 14  17  7
  4Q LOSS WILD-TYPE 22 36  33 18
D46V8, multiclass
D46V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3   43
  4Q LOSS WILD-TYPE    3  113
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                3                 3
  YES              43               113

Clustering(47) Variable = 5p loss mutation analysis
D47V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     6   0
  5P LOSS WILD-TYPE 108  11
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6               119 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                11 
$`5P LOSS MUTATED`
TCGA-AF-2687 TCGA-AG-3999 TCGA-AG-A01W TCGA-DC-6155 TCGA-DY-A0XA TCGA-EI-6885 
       19.53         1.02        70.03         7.36       119.51         5.23 

$`5P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       15.85        11.77        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 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 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-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        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-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01         9.99         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        6.97        27.91         6.97        19.99         5.92         3.98 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.00         0.26        41.33        57.24       121.08        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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
        7.10         6.15         3.55         3.98         2.73         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        2.76         2.04         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        47.70        47.08        20.91 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.02              0.16 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           119.51            121.08 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           13.445             6.150 
[1] "1.0 - 119.5 (13.4)" "0.2 - 121.1 (6.2)" 
       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 WILD-TYPE" 
       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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" 
       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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" 
       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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"5P LOSS WILD-TYPE" 
[1] "hr="     "2.5e+08"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      8    3
  5P LOSS WILD-TYPE   66   85
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               8                66
  MALE                 3                85
D47V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     11    0
  5P LOSS WILD-TYPE  132   13
                                clus
vv                               5P LOSS MUTATED 5P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       11               132
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED     0   2   9   0
  5P LOSS WILD-TYPE   9  27 100  14
D47V5, multiclass
                   vv
clus                N0 N1 N2
  5P LOSS MUTATED    5  2  4
  5P LOSS WILD-TYPE 78 43 28
D47V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  5P LOSS MUTATED     9   2   0   0
  5P LOSS WILD-TYPE 114  20   2  13
D47V7, multiclass
                   vv
clus                 I II III IV
  5P LOSS MUTATED    1  4   4  2
  5P LOSS WILD-TYPE 29 46  46 23
D47V8, multiclass
D47V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1   10
  5P LOSS WILD-TYPE    5  146
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                1                 5
  YES              10               146

Clustering(48) Variable = 5q loss mutation analysis
D48V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    11   3
  5Q LOSS WILD-TYPE 103   8
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               14               111 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                 8 
$`5Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-6672 TCGA-AG-3999 TCGA-AG-A01W TCGA-AG-A01Y 
       19.53        17.62         7.33         1.02        70.03        63.98 
TCGA-AG-A026 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A0XA TCGA-DY-A1DD 
        1.94        10.19         7.36         6.97       119.51        57.24 
TCGA-DY-A1DG TCGA-F5-6702 
       51.48         2.17 

$`5Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       15.85        11.77        10.62        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 
       10.39        14.50         8.45         7.59         6.35         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         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-4001 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-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-A020 
       13.02         1.02         1.02        12.00        12.00        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       51.98        49.94        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-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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        8.98        27.91         6.97        19.99         5.92         3.98 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
        5.00         0.26        41.33       121.08        24.13        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40         7.63         0.16         2.17         8.22 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
        0.46         3.98         0.66         6.90         7.10         6.15 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        3.55         3.98         2.73         5.23         7.79         2.76 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        2.04         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-G5-6572 TCGA-G5-6641 
       47.70        47.08        20.91 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.02              0.16 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           119.51            121.08 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           13.905             6.020 
[1] "1.0 - 119.5 (13.9)" "0.2 - 121.1 (6.0)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "5Q LOSS WILD-TYPE" 
       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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "5Q LOSS WILD-TYPE" 
       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 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"5Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"5Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     13   10
  5Q LOSS WILD-TYPE   61   78
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              13                61
  MALE                10                78
D48V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     21    1
  5Q LOSS WILD-TYPE  122   12
                                clus
vv                               5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       21               122
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    0  3 17  3
  5Q LOSS WILD-TYPE  9 26 92 11
D48V5, multiclass
                   vv
clus                N0 N1 N2
  5Q LOSS MUTATED   11  6  6
  5Q LOSS WILD-TYPE 72 39 26
D48V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  5Q LOSS MUTATED    16   3   1   2
  5Q LOSS WILD-TYPE 107  19   1  11
D48V7, multiclass
                   vv
clus                 I II III IV
  5Q LOSS MUTATED    2  9   7  5
  5Q LOSS WILD-TYPE 28 41  43 20
D48V8, multiclass
D48V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4   19
  5Q LOSS WILD-TYPE    2  137
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                4                 2
  YES              19               137

Clustering(49) Variable = 6p loss mutation analysis
D49V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED     5   1
  6P LOSS WILD-TYPE 109  10
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6               119 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                10 
$`6P LOSS MUTATED`
TCGA-AF-2692 TCGA-AG-A008 TCGA-AG-A011 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6883 
       13.55        13.91        17.03         0.26        24.13         3.98 

$`6P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       19.53        15.85        11.77        10.62        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-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         9.99         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        3.98         5.00       119.51        41.33        57.24       121.08 
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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
        7.10         6.15         3.55         2.73         5.23         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        2.76         2.04         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        47.70        47.08        20.91 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.26              0.16 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            24.13            121.08 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            13.73              6.15 
[1] "0.3 - 24.1 (13.7)" "0.2 - 121.1 (6.2)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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 WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"6P LOSS WILD-TYPE" 
[1] "hr=" "5.5"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    4
  6P LOSS WILD-TYPE   70   84
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               4                70
  MALE                 4                84
D49V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5    2
  6P LOSS WILD-TYPE  138   11
                                clus
vv                               6P LOSS MUTATED 6P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               138
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED     0   1   7   0
  6P LOSS WILD-TYPE   9  28 102  14
D49V5, multiclass
                   vv
clus                N0 N1 N2
  6P LOSS MUTATED    6  0  2
  6P LOSS WILD-TYPE 77 45 30
D49V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  6P LOSS MUTATED     7   1   0   0
  6P LOSS WILD-TYPE 116  21   2  13
D49V7, multiclass
                   vv
clus                 I II III IV
  6P LOSS MUTATED    1  5   1  1
  6P LOSS WILD-TYPE 29 45  49 24
D49V8, multiclass
D49V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    8
  6P LOSS WILD-TYPE    6  148
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                0                 6
  YES               8               148

Clustering(50) Variable = 6q loss mutation analysis
D50V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED     7   0
  6Q LOSS WILD-TYPE 107  11
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                7               118 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                0                11 
$`6Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AF-2693 TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 TCGA-DT-5265 
       13.55        19.10        13.91        17.03         0.49         0.26 
TCGA-EI-6883 
        3.98 

$`6Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 
       19.53        15.85        11.77        10.62        12.72        17.62 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45         7.59         6.35         7.33 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        1.02         1.02         2.01         1.02         0.99         1.02 
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-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-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
        0.99        20.94         6.02        25.94        23.01        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-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.94        40.96        38.01         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-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01         9.99         5.03         8.98         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.91         6.97        19.99         5.92         3.98         5.00 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      119.51        41.33        57.24       121.08        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         7.63         0.16         2.17 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
        8.22         0.46         3.98         0.66         6.90         7.10 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        6.15         3.55         2.73         5.23         7.79         2.76 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        2.04         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        47.70        47.08        20.91 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.26              0.16 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            19.10            121.08 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            13.55              6.25 
[1] "0.3 - 19.1 (13.6)" "0.2 - 121.1 (6.2)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "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-3581        TCGA-AG-3582 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"6Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "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-3581        TCGA-AG-3582 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"6Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "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-3581        TCGA-AG-3582 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"6Q LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    9
  6Q LOSS WILD-TYPE   69   79
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               5                69
  MALE                 9                79
D50V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      9    3
  6Q LOSS WILD-TYPE  134   10
                                clus
vv                               6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        9               134
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    0  2 12  0
  6Q LOSS WILD-TYPE  9 27 97 14
D50V5, multiclass
                   vv
clus                N0 N1 N2
  6Q LOSS MUTATED    9  1  4
  6Q LOSS WILD-TYPE 74 44 28
D50V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  6Q LOSS MUTATED    10   3   0   1
  6Q LOSS WILD-TYPE 113  19   2  12
D50V7, multiclass
                   vv
clus                 I II III IV
  6Q LOSS MUTATED    2  7   2  2
  6Q LOSS WILD-TYPE 28 43  48 23
D50V8, multiclass
D50V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   14
  6Q LOSS WILD-TYPE    6  142
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 6
  YES              14               142

Clustering(51) Variable = 8p loss mutation analysis
D51V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   39  2
  8P LOSS WILD-TYPE 75  9
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               41                84 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 9 
$`8P LOSS MUTATED`
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-6136 
       11.77        10.62        13.55        19.10        17.62         7.59 
TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-3999 
        7.33         1.02         0.95         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
        1.02         1.02        25.94        23.01        17.03        15.91 
TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 TCGA-CL-4957 
        1.02         1.94        38.93        40.96        10.19        13.97 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6683 
       60.00        10.98        11.01         7.36        27.91         5.00 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-7002 
        0.26       119.51       121.08         2.40         3.98         2.76 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6641 
        2.04         0.85         0.69         0.46        20.91 

$`8P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.53        15.85        12.72        10.39        14.50         8.45 
TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        6.35         1.02         2.01         1.02         0.99         1.02 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4007 
        1.02         0.99         0.92         1.02         0.99         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A016 
        0.99        20.94        13.91         6.02        13.02         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-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       49.94        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-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        9.37         4.70         7.99         9.99         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC 
        6.97         6.97        19.99         5.92         3.98        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         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
        0.16         2.17         8.22         0.46         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        7.79         3.39         2.17         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        47.70        47.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.26              0.16 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           121.08             70.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             7.59              6.02 
[1] "0.3 - 121.1 (7.6)" "0.2 - 70.0 (6.0)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "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 WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G5-6641 
  "8P LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "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 WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G5-6641 
  "8P LOSS MUTATED" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "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 WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3581        TCGA-AG-3582 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G5-6641 
  "8P LOSS MUTATED" 
[1] "hr=" "2.3"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     24   32
  8P LOSS WILD-TYPE   50   56
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              24                50
  MALE                32                56
D51V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     50    4
  8P LOSS WILD-TYPE   93    9
                                clus
vv                               8P LOSS MUTATED 8P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       50                93
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    3 10 37  6
  8P LOSS WILD-TYPE  6 19 72  8
D51V5, multiclass
                   vv
clus                N0 N1 N2
  8P LOSS MUTATED   28 16 12
  8P LOSS WILD-TYPE 55 29 20
D51V6, multiclass
                   vv
clus                M0 M1 M1A MX
  8P LOSS MUTATED   44  5   0  6
  8P LOSS WILD-TYPE 79 17   2  7
D51V7, multiclass
                   vv
clus                 I II III IV
  8P LOSS MUTATED   10 18  20  7
  8P LOSS WILD-TYPE 20 32  30 18
D51V8, multiclass
D51V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4   52
  8P LOSS WILD-TYPE    2  104
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4                 2
  YES              52               104

Clustering(52) Variable = 8q loss mutation analysis
D52V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     2   0
  8Q LOSS WILD-TYPE 112  11
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               123 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                11 
$`8Q LOSS MUTATED`
TCGA-AG-A02X TCGA-DC-6157 
       40.96        27.91 

$`8Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-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-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         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
        5.03         8.98         7.36         6.97         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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 
       47.70        47.08        20.91 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            27.91              0.16 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            40.96            121.08 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           34.435             6.150 
[1] "27.9 - 41.0 (34.4)" "0.2 - 121.1 (6.2)" 
       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-3581        TCGA-AG-3582 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"8Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2               123 
       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-3581        TCGA-AG-3582 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A032        TCGA-AH-6544        TCGA-AH-6547 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6622 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957        TCGA-CL-5917 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D52V2, continuous
D52V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    2
  8Q LOSS WILD-TYPE   73   86
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               1                73
  MALE                 2                86
D52V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    0
  8Q LOSS WILD-TYPE  140   13
                                clus
vv                               8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        3               140
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED     0   2   1   0
  8Q LOSS WILD-TYPE   9  27 108  14
D52V5, multiclass
                   vv
clus                N0 N1 N2
  8Q LOSS MUTATED    2  1  0
  8Q LOSS WILD-TYPE 81 44 32
D52V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  8Q LOSS MUTATED     2   1   0   0
  8Q LOSS WILD-TYPE 121  21   2  13
D52V7, multiclass
                   vv
clus                 I II III IV
  8Q LOSS MUTATED    2  0   0  1
  8Q LOSS WILD-TYPE 28 50  50 24
D52V8, multiclass
D52V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    3
  8Q LOSS WILD-TYPE    6  153
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 6
  YES               3               153

Clustering(53) Variable = 9p loss mutation analysis
D53V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED     5   3
  9P LOSS WILD-TYPE 109   8
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                8               117 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                 8 
$`9P LOSS MUTATED`
TCGA-AG-3583 TCGA-AG-A026 TCGA-AG-A02G TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6158 
        2.01         1.94        38.93        13.97        11.01         6.97 
TCGA-DY-A1DG TCGA-EI-6514 
       51.48         7.10 

$`9P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3599 
        6.35         7.33         1.02         1.02         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.94        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-5917 TCGA-CL-5918 
        6.02         6.94         9.37         4.70        60.00         7.99 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98         9.99         5.03         8.98         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.91        19.99         5.92         3.98         5.00         0.26 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      119.51        41.33        57.24       121.08        24.13        32.58 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40         7.63         0.16         2.17         8.22 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
        0.46         3.98         0.66         6.90         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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 
       47.70        47.08        20.91 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.94              0.16 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            51.48            121.08 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            9.055             6.020 
[1] "1.9 - 51.5 (9.1)"  "0.2 - 121.1 (6.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P LOSS WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"9P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P LOSS WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"9P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P LOSS WILD-TYPE" "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 WILD-TYPE" "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-3581        TCGA-AG-3582 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9P LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6641 
"9P LOSS WILD-TYPE" 
[1] "hr=" "4.7"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      5    7
  9P LOSS WILD-TYPE   69   81
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               5                69
  MALE                 7                81
D53V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     11    1
  9P LOSS WILD-TYPE  132   12
                                clus
vv                               9P LOSS MUTATED 9P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       11               132
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED     0   4   7   1
  9P LOSS WILD-TYPE   9  25 102  13
D53V5, multiclass
                   vv
clus                N0 N1 N2
  9P LOSS MUTATED    6  3  3
  9P LOSS WILD-TYPE 77 42 29
D53V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  9P LOSS MUTATED     8   4   0   0
  9P LOSS WILD-TYPE 115  18   2  13
D53V7, multiclass
                   vv
clus                 I II III IV
  9P LOSS MUTATED    3  3   2  4
  9P LOSS WILD-TYPE 27 47  48 21
D53V8, multiclass
D53V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   12
  9P LOSS WILD-TYPE    6  144
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                0                 6
  YES              12               144

Clustering(54) Variable = 9q loss mutation analysis
D54V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED     6   2
  9Q LOSS WILD-TYPE 108   9
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8               117 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                 9 
$`9Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AG-3583 TCGA-AG-A026 TCGA-AG-A02G TCGA-CL-4957 TCGA-DC-4749 
       13.55         2.01         1.94        38.93        13.97        11.01 
TCGA-DC-6158 TCGA-EI-6514 
        6.97         7.10 

$`9Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       19.53        15.85        11.77        10.62        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        7.33         1.02         1.02         1.02         0.99         1.02 
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-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-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        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-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-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.94         9.37         4.70        60.00         7.99        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        9.99         5.03         8.98         7.36         6.97        27.91 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.92         3.98         5.00         0.26       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.33        57.24       121.08        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         7.63         0.16         2.17         8.22 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
        0.46         3.98         0.66         6.90         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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 
       47.70        47.08        20.91 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             1.94              0.16 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            38.93            121.08 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            9.055             6.020 
[1] "1.9 - 38.9 (9.1)"  "0.2 - 121.1 (6.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q LOSS WILD-TYPE" "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-3581        TCGA-AG-3582 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"9Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q LOSS WILD-TYPE" "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-3581        TCGA-AG-3582 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"9Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q LOSS WILD-TYPE" "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-3581        TCGA-AG-3582 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"9Q LOSS WILD-TYPE" "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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6641 
"9Q LOSS WILD-TYPE" 
[1] "hr=" "7.3"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5    6
  9Q LOSS WILD-TYPE   69   82
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               5                69
  MALE                 6                82
D54V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9    1
  9Q LOSS WILD-TYPE  134   12
                                clus
vv                               9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        9               134
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED     0   4   5   2
  9Q LOSS WILD-TYPE   9  25 104  12
D54V5, multiclass
                   vv
clus                N0 N1 N2
  9Q LOSS MUTATED    7  3  1
  9Q LOSS WILD-TYPE 76 42 31
D54V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  9Q LOSS MUTATED     9   2   0   0
  9Q LOSS WILD-TYPE 114  20   2  13
D54V7, multiclass
                   vv
clus                 I II III IV
  9Q LOSS MUTATED    3  4   2  2
  9Q LOSS WILD-TYPE 27 46  48 23
D54V8, multiclass
D54V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0   11
  9Q LOSS WILD-TYPE    6  145
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                0                 6
  YES              11               145

Clustering(55) Variable = 10p loss mutation analysis
D55V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    14   0
  10P LOSS WILD-TYPE 100  11
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                14                111 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                 11 
$`10P LOSS MUTATED`
TCGA-AF-6672 TCGA-AG-3887 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X 
        7.33         0.92        13.91        12.00        10.98        40.96 
TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EF-5830 
        0.49         7.36        27.91         5.00       121.08         0.49 
TCGA-EI-6513 TCGA-EI-7004 
        6.90         2.04 

$`10P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        6.35         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 
        1.02         0.95         1.02         0.99         0.99         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-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-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.01         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         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03         8.98         6.97         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        3.98         0.26       119.51        41.33        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.58         2.40         7.63         0.16         2.17 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 
        8.22         0.46         3.98         0.66         7.10         6.15 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        3.55         3.98         2.73         5.23         7.79         2.76 
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 
       47.70        47.08        20.91 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.49               0.16 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            121.08             119.51 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             7.345              6.020 
[1] "0.5 - 121.1 (7.3)" "0.2 - 119.5 (6.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P LOSS WILD-TYPE" "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 WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P LOSS WILD-TYPE" "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 WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P LOSS WILD-TYPE" "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 WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr="     "2.2e+08"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8    9
  10P LOSS WILD-TYPE   66   79
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                8                 66
  MALE                  9                 79
D55V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     13    4
  10P LOSS WILD-TYPE  130    9
                                clus
vv                               10P LOSS MUTATED 10P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        13                130
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    0  4 10  3
  10P LOSS WILD-TYPE  9 25 99 11
D55V5, multiclass
                    vv
clus                 N0 N1 N2
  10P LOSS MUTATED    8  7  2
  10P LOSS WILD-TYPE 75 38 30
D55V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  10P LOSS MUTATED    15   1   0   1
  10P LOSS WILD-TYPE 108  21   2  12
D55V7, multiclass
                    vv
clus                  I II III IV
  10P LOSS MUTATED    3  5   6  2
  10P LOSS WILD-TYPE 27 45  44 23
D55V8, multiclass
D55V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   16
  10P LOSS WILD-TYPE    5  140
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                  5
  YES               16                140

Clustering(56) Variable = 10q loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   15  1
  10Q LOSS WILD-TYPE 99 10
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                16                109 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                 10 
$`10Q LOSS MUTATED`
TCGA-AF-6672 TCGA-AG-3887 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A020 
        7.33         0.92        13.91        17.03        12.00        10.98 
TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EF-5830 
       40.96         7.36        27.91         5.00       121.08         0.49 
TCGA-EI-6513 TCGA-EI-7002 TCGA-F5-6812 TCGA-G5-6572 
        6.90         2.76         0.66        47.08 

$`10Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        6.35         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 
        1.02         0.95         1.02         0.99         0.99         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-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
        0.99        20.94         6.02        25.94        23.01        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-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         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03         8.98         6.97         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        3.98         0.26       119.51        41.33        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.58         2.40         7.63         0.16         2.17 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 
        8.22         0.46         3.98         0.66         7.10         6.15 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        3.55         3.98         2.73         5.23         7.79         2.04 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        3.39         0.85         2.17         0.39         1.02         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        47.70 
TCGA-G5-6641 
       20.91 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.49               0.16 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            121.08             119.51 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              9.17               6.02 
[1] "0.5 - 121.1 (9.2)" "0.2 - 119.5 (6.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q LOSS WILD-TYPE" "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 WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q LOSS WILD-TYPE" "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 WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q LOSS WILD-TYPE" "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 WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      8   13
  10Q LOSS WILD-TYPE   66   75
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                8                 66
  MALE                 13                 75
D56V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     17    4
  10Q LOSS WILD-TYPE  126    9
                                clus
vv                               10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        17                126
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    0  4 14  2
  10Q LOSS WILD-TYPE  9 25 95 12
D56V5, multiclass
                    vv
clus                 N0 N1 N2
  10Q LOSS MUTATED   11  6  3
  10Q LOSS WILD-TYPE 72 39 29
D56V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  10Q LOSS MUTATED    18   1   0   1
  10Q LOSS WILD-TYPE 105  21   2  12
D56V7, multiclass
                    vv
clus                  I II III IV
  10Q LOSS MUTATED    3  8   7  2
  10Q LOSS WILD-TYPE 27 42  43 23
D56V8, multiclass
D56V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   20
  10Q LOSS WILD-TYPE    5  136
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 1                  5
  YES               20                136

Clustering(57) Variable = 11p loss mutation analysis
D57V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    12   1
  11P LOSS WILD-TYPE 102  10
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                112 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 10 
$`11P LOSS MUTATED`
TCGA-AF-6136 TCGA-AG-3581 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X 
        7.59         1.02        13.91        12.00        10.98        40.96 
TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 
        0.49         0.69         7.36         0.26        24.13         8.22 
TCGA-F5-6813 
        0.69 

$`11P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         6.35 
TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        7.33         1.02         2.01         1.02         0.99         1.02 
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-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-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-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       38.01         1.45         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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        8.98         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        3.98         5.00       119.51        41.33        57.24       121.08 
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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
        2.17         0.46         3.98         0.66         6.90         7.10 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
        6.15         3.55         3.98         2.73         5.23         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        2.76         2.04         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        47.70        47.08        20.91 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.26               0.16 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             40.96             121.08 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             7.590              6.085 
[1] "0.3 - 41.0 (7.6)"  "0.2 - 121.1 (6.1)"
        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 WILD-TYPE" "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 WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11P LOSS WILD-TYPE" "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 WILD-TYPE" "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 WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11P LOSS WILD-TYPE" "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 WILD-TYPE" "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 WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     10    9
  11P LOSS WILD-TYPE   64   79
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               10                 64
  MALE                  9                 79
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     14    4
  11P LOSS WILD-TYPE  129    9
                                clus
vv                               11P LOSS MUTATED 11P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        14                129
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    0  5 13  1
  11P LOSS WILD-TYPE  9 24 96 13
D57V5, multiclass
                    vv
clus                 N0 N1 N2
  11P LOSS MUTATED    8  6  5
  11P LOSS WILD-TYPE 75 39 27
D57V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  11P LOSS MUTATED    17   1   0   1
  11P LOSS WILD-TYPE 106  21   2  12
D57V7, multiclass
                    vv
clus                  I II III IV
  11P LOSS MUTATED    4  4  10  0
  11P LOSS WILD-TYPE 26 46  40 25
D57V8, multiclass
D57V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1   18
  11P LOSS WILD-TYPE    5  138
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 1                  5
  YES               18                138

Clustering(58) Variable = 11q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   16  1
  11Q LOSS WILD-TYPE 98 10
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                17                108 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                 10 
$`11Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-A008 
       13.55        19.10         7.59         7.33         1.02        13.91 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CL-4957 
       12.00        10.98         0.49         0.69        10.19        13.97 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 
        7.36         6.97         0.26        24.13         8.22 

$`11Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 
       19.53        15.85        11.77        10.62        12.72        17.62 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3582 TCGA-AG-3583 
       10.39        14.50         8.45         6.35         1.02         2.01 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        1.02         0.99         1.02         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-A00C 
        1.02         1.02         1.02         0.99        20.94         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-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        70.03        63.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
        1.94        38.93        61.94        40.96        38.01         1.45 
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-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37         4.70        60.00         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
        9.99         5.03         8.98         6.97        27.91        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.92         3.98         5.00       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      121.08        51.48        32.58         0.49         2.40         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        0.16         2.17         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        7.79         2.76         2.04         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        47.70        47.08        20.91 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.26               0.16 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             24.13             121.08 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              8.22               5.97 
[1] "0.3 - 24.1 (8.2)"  "0.2 - 121.1 (6.0)"
        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 WILD-TYPE"   "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 WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11Q LOSS WILD-TYPE" "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 WILD-TYPE"   "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 WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11Q LOSS WILD-TYPE" "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 WILD-TYPE"   "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 WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12   11
  11Q LOSS WILD-TYPE   62   77
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               12                 62
  MALE                 11                 77
D58V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     15    5
  11Q LOSS WILD-TYPE  128    8
                                clus
vv                               11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        15                128
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    0  6 16  1
  11Q LOSS WILD-TYPE  9 23 93 13
D58V5, multiclass
                    vv
clus                 N0 N1 N2
  11Q LOSS MUTATED   11  8  4
  11Q LOSS WILD-TYPE 72 37 28
D58V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  11Q LOSS MUTATED    18   1   0   3
  11Q LOSS WILD-TYPE 105  21   2  10
D58V7, multiclass
                    vv
clus                  I II III IV
  11Q LOSS MUTATED    5  6  10  1
  11Q LOSS WILD-TYPE 25 44  40 24
D58V8, multiclass
D58V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   20
  11Q LOSS WILD-TYPE    3  136
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 3                  3
  YES               20                136

Clustering(59) Variable = 12p loss mutation analysis
D59V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     3   3
  12P LOSS WILD-TYPE 111   8
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                119 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                  8 
$`12P LOSS MUTATED`
TCGA-AF-3913 TCGA-AG-A01W TCGA-DC-6155 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 
       10.39        70.03         7.36        24.13        51.48         2.17 

$`12P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        10.62        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        17.62        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        12.00        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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        8.98         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      121.08        32.58         0.49         2.40         7.63         0.16 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
        8.22         0.46         3.98         0.66         6.90         7.10 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
        6.15         3.55         3.98         2.73         5.23         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        2.76         2.04         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        47.70        47.08        20.91 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2.17               0.16 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             70.03             121.08 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             17.26               6.02 
[1] "2.2 - 70.0 (17.3)" "0.2 - 121.1 (6.0)"
        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 WILD-TYPE" "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 WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12P LOSS WILD-TYPE" "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 WILD-TYPE" "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 WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12P LOSS WILD-TYPE" "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 WILD-TYPE" "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 WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "2.4"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      9    3
  12P LOSS WILD-TYPE   65   85
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                9                 65
  MALE                  3                 85
D59V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12    0
  12P LOSS WILD-TYPE  131   13
                                clus
vv                               12P LOSS MUTATED 12P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        12                131
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    0  1 11  0
  12P LOSS WILD-TYPE  9 28 98 14
D59V5, multiclass
                    vv
clus                 N0 N1 N2
  12P LOSS MUTATED    4  5  3
  12P LOSS WILD-TYPE 79 40 29
D59V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  12P LOSS MUTATED     9   3   0   0
  12P LOSS WILD-TYPE 114  19   2  13
D59V7, multiclass
                    vv
clus                  I II III IV
  12P LOSS MUTATED    0  4   5  2
  12P LOSS WILD-TYPE 30 46  45 23
D59V8, multiclass
D59V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   12
  12P LOSS WILD-TYPE    6  144
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                  6
  YES               12                144

Clustering(60) Variable = 12q loss mutation analysis
D60V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     3   2
  12Q LOSS WILD-TYPE 111   9
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 5                120 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 2                  9 
$`12Q LOSS MUTATED`
TCGA-AG-A014 TCGA-AH-6544 TCGA-DC-6155 TCGA-DY-A1DF TCGA-DY-A1DG 
       15.91         0.49         7.36        24.13        51.48 

$`12Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.94        23.01        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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        8.98         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      121.08        32.58         0.49         2.40         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        7.79         2.76         2.04         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        47.70        47.08        20.91 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.49               0.16 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             51.48             121.08 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            15.910              6.085 
[1] "0.5 - 51.5 (15.9)" "0.2 - 121.1 (6.1)"
        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 WILD-TYPE" "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 WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12Q LOSS WILD-TYPE" "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 WILD-TYPE" "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 WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12Q LOSS WILD-TYPE" "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 WILD-TYPE" "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 WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "3.5"
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4    4
  12Q LOSS WILD-TYPE   70   84
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                4                 70
  MALE                  4                 84
D60V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8    0
  12Q LOSS WILD-TYPE  135   13
                                clus
vv                               12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         8                135
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     0   2   6   0
  12Q LOSS WILD-TYPE   9  27 103  14
D60V5, multiclass
                    vv
clus                 N0 N1 N2
  12Q LOSS MUTATED    2  4  2
  12Q LOSS WILD-TYPE 81 41 30
D60V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  12Q LOSS MUTATED     5   3   0   0
  12Q LOSS WILD-TYPE 118  19   2  13
D60V7, multiclass
                    vv
clus                  I II III IV
  12Q LOSS MUTATED    1  1   3  2
  12Q LOSS WILD-TYPE 29 49  47 23
D60V8, multiclass
D60V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    8
  12Q LOSS WILD-TYPE    6  148
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 0                  6
  YES                8                148

Clustering(61) Variable = 13q loss mutation analysis
D61V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     2   0
  13Q LOSS WILD-TYPE 112  11
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                123 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                 11 
$`13Q LOSS MUTATED`
TCGA-DC-6156 TCGA-DY-A0XA 
        6.97       119.51 

$`13Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-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-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-6157 TCGA-DC-6158 
        9.99         5.03         8.98         7.36        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.92         3.98         5.00         0.26        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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 
       47.70        47.08        20.91 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              6.97               0.16 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            119.51             121.08 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             63.24               6.15 
[1] "7.0 - 119.5 (63.2)" "0.2 - 121.1 (6.2)" 
        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-3581 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"13Q LOSS WILD-TYPE" "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-3581 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"13Q LOSS WILD-TYPE" "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-3581 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                123 
        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-3581 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6157         TCGA-DC-6158 
"13Q LOSS WILD-TYPE" "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-A1DC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6514         TCGA-EI-6881         TCGA-EI-6882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6883         TCGA-EI-6884         TCGA-EI-6885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6917         TCGA-EI-7002         TCGA-EI-7004 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6810         TCGA-F5-6811         TCGA-F5-6812 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6813         TCGA-F5-6814         TCGA-F5-6861 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6863         TCGA-F5-6864         TCGA-G5-6233 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6235         TCGA-G5-6572         TCGA-G5-6641 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    3
  13Q LOSS WILD-TYPE   72   85
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                 72
  MALE                  3                 85
D61V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    1
  13Q LOSS WILD-TYPE  139   12
                                clus
vv                               13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         4                139
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED     0   0   4   1
  13Q LOSS WILD-TYPE   9  29 105  13
D61V5, multiclass
                    vv
clus                 N0 N1 N2
  13Q LOSS MUTATED    3  0  2
  13Q LOSS WILD-TYPE 80 45 30
D61V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  13Q LOSS MUTATED     4   0   1   0
  13Q LOSS WILD-TYPE 119  22   1  13
D61V7, multiclass
                    vv
clus                  I II III IV
  13Q LOSS MUTATED    0  3   1  1
  13Q LOSS WILD-TYPE 30 47  49 24
D61V8, multiclass
D61V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0    5
  13Q LOSS WILD-TYPE    6  151
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 0                  6
  YES                5                151

Clustering(62) Variable = 14q loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   36  3
  14Q LOSS WILD-TYPE 78  8
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                39                 86 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                  8 
$`14Q LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AG-3582 TCGA-AG-3727 
       15.85        11.77        13.55        17.62         1.02         0.95 
TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H 
        0.99         0.99         1.02         1.02         6.02        25.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6620 
        1.94        38.93        38.01         0.49        10.19         6.02 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
        9.37        13.97         7.99        11.01         5.03         7.36 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 
       27.91         6.97         5.00       121.08        51.48         7.63 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 
        6.90         7.10         6.15         2.73         2.76         0.85 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        0.39         1.02         0.66 

$`14Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       19.53        10.62        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 
        8.45         7.59         6.35         7.33         1.02         2.01 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.99         1.02         1.02         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3999 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-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.91        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-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
       51.98        49.94        61.94        40.96         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
        0.72         4.60         1.81         6.02         6.94         4.70 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
       60.00        10.98         9.99         8.98         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.92         3.98         0.26       119.51        41.33        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.58         0.49         2.40         0.16         2.17 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
        8.22         0.46         3.98         0.66         3.55         3.98 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 
        5.23         7.79         2.04         3.39         2.17         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.39               0.16 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            121.08             119.51 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             6.900              6.185 
[1] "0.4 - 121.1 (6.9)" "0.2 - 119.5 (6.2)"
        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-3581 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        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-3581 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        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-3581 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     22   29
  14Q LOSS WILD-TYPE   52   59
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               22                 52
  MALE                 29                 59
D62V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     49    0
  14Q LOSS WILD-TYPE   94   13
                                clus
vv                               14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        49                 94
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    2  7 40  2
  14Q LOSS WILD-TYPE  7 22 69 12
D62V5, multiclass
                    vv
clus                 N0 N1 N2
  14Q LOSS MUTATED   26 18  7
  14Q LOSS WILD-TYPE 57 27 25
D62V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  14Q LOSS MUTATED   40  8   0  2
  14Q LOSS WILD-TYPE 83 14   2 11
D62V7, multiclass
                    vv
clus                  I II III IV
  14Q LOSS MUTATED    7 19  16  6
  14Q LOSS WILD-TYPE 23 31  34 19
D62V8, multiclass
D62V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   49
  14Q LOSS WILD-TYPE    4  107
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 2                  4
  YES               49                107

Clustering(63) Variable = 15q loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   37  5
  15Q LOSS WILD-TYPE 77  6
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                42                 83 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                  6 
$`15Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3583 
       13.55        17.62        14.50         7.33         1.02         2.01 
TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H 
        0.99         0.99         1.02         1.02        13.91        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       23.01        17.03         1.02         1.94        38.93        40.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5918 
       38.01         0.49         0.69        10.19         9.37         7.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 
        7.36        27.91        41.33        57.24        24.13         0.49 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        2.40         3.98         7.10         6.15         3.98         2.73 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        5.23         2.76         0.85         1.02         0.66         0.69 

$`15Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       19.53        15.85        11.77        10.62        19.10        12.72 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3587 
       10.39         8.45         7.59         6.35         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3887 
        0.99         1.02         0.95         1.02         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
        1.02         0.99         1.02         1.02         0.99        20.94 
TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N 
        6.02        15.91        13.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       70.03        63.98        10.98        51.98        49.94        61.94 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.72         4.60         1.81         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
        6.94         4.70        13.97        60.00        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
        9.99         5.03         8.98         6.97         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
        5.92         3.98         5.00         0.26       119.51       121.08 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.58         7.63         0.16         2.17         8.22 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        0.46         0.66         6.90         3.55         7.79         2.04 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        3.39         2.17         0.39         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        47.70        47.08        20.91 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.49               0.16 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             57.24             121.08 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              5.69               6.90 
[1] "0.5 - 57.2 (5.7)"  "0.2 - 121.1 (6.9)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"15Q LOSS WILD-TYPE"   "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-3581 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"15Q LOSS WILD-TYPE"   "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-3581 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"15Q LOSS WILD-TYPE"   "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-3581 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED"   "15Q LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "3"  
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     24   34
  15Q LOSS WILD-TYPE   50   54
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               24                 50
  MALE                 34                 54
D63V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     51    4
  15Q LOSS WILD-TYPE   92    9
                                clus
vv                               15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        51                 92
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    2  6 45  5
  15Q LOSS WILD-TYPE  7 23 64  9
D63V5, multiclass
                    vv
clus                 N0 N1 N2
  15Q LOSS MUTATED   28 17 13
  15Q LOSS WILD-TYPE 55 28 19
D63V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  15Q LOSS MUTATED   44  8   0  5
  15Q LOSS WILD-TYPE 79 14   2  8
D63V7, multiclass
                    vv
clus                  I II III IV
  15Q LOSS MUTATED    6 22  20  9
  15Q LOSS WILD-TYPE 24 28  30 16
D63V8, multiclass
D63V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3   55
  15Q LOSS WILD-TYPE    3  101
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 3                  3
  YES               55                101

Clustering(64) Variable = 16p loss mutation analysis
D64V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     2   0
  16P LOSS WILD-TYPE 112  11
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                123 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                 11 
$`16P LOSS MUTATED`
TCGA-DC-6682 TCGA-F5-6811 
        3.98         1.02 

$`16P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-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-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 
        9.99         5.03         8.98         7.36         6.97        27.91 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        6.97        19.99         5.92         5.00         0.26       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.33        57.24       121.08        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         7.63         0.16         2.17         8.22 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
        0.46         3.98         0.66         6.90         7.10         6.15 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        3.55         3.98         2.73         5.23         7.79         2.76 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
        2.04         3.39         0.85         2.17         0.39         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 
       47.70        47.08        20.91 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              1.02               0.16 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              3.98             121.08 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               2.5                6.9 
[1] "1.0 - 4.0 (2.5)"   "0.2 - 121.1 (6.9)"
        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-3581 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16P LOSS WILD-TYPE" "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-3581 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16P LOSS WILD-TYPE" "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-3581 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                123 
        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-3581 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        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-F5-6812 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6813         TCGA-F5-6814         TCGA-F5-6861 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6863         TCGA-F5-6864         TCGA-G5-6233 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6235         TCGA-G5-6572         TCGA-G5-6641 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    2
  16P LOSS WILD-TYPE   70   86
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                4                 70
  MALE                  2                 86
D64V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    1
  16P LOSS WILD-TYPE  139   12
                                clus
vv                               16P LOSS MUTATED 16P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         4                139
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     0   0   6   0
  16P LOSS WILD-TYPE   9  29 103  14
D64V5, multiclass
                    vv
clus                 N0 N1 N2
  16P LOSS MUTATED    5  0  1
  16P LOSS WILD-TYPE 78 45 31
D64V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  16P LOSS MUTATED     5   1   0   0
  16P LOSS WILD-TYPE 118  21   2  13
D64V7, multiclass
                    vv
clus                  I II III IV
  16P LOSS MUTATED    0  5   0  1
  16P LOSS WILD-TYPE 30 45  50 24
D64V8, multiclass
D64V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    6
  16P LOSS WILD-TYPE    6  150
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                  6
  YES                6                150

Clustering(65) Variable = 16q loss mutation analysis
D65V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     3   0
  16Q LOSS WILD-TYPE 111  11
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                122 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                 11 
$`16Q LOSS MUTATED`
TCGA-AF-6672 TCGA-DC-6682 TCGA-F5-6811 
        7.33         3.98         1.02 

$`16Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        6.35         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98         7.36         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.92         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       121.08        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         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        3.98         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.98         2.73         5.23         7.79         2.76         2.04 
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-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.08         0.76         0.46        18.25        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              1.02               0.16 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              7.33             121.08 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             3.980              6.625 
[1] "1.0 - 7.3 (4.0)"   "0.2 - 121.1 (6.6)"
        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-3581 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16Q LOSS WILD-TYPE" "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-3581 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16Q LOSS WILD-TYPE" "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-3581 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr="     "3400000"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    5
  16Q LOSS WILD-TYPE   69   83
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                5                 69
  MALE                  5                 83
D65V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8    1
  16Q LOSS WILD-TYPE  135   12
                                clus
vv                               16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         8                135
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     0   2   7   1
  16Q LOSS WILD-TYPE   9  27 102  13
D65V5, multiclass
                    vv
clus                 N0 N1 N2
  16Q LOSS MUTATED    7  0  3
  16Q LOSS WILD-TYPE 76 45 29
D65V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  16Q LOSS MUTATED     8   1   0   1
  16Q LOSS WILD-TYPE 115  21   2  12
D65V7, multiclass
                    vv
clus                  I II III IV
  16Q LOSS MUTATED    2  5   1  2
  16Q LOSS WILD-TYPE 28 45  49 23
D65V8, multiclass
D65V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    9
  16Q LOSS WILD-TYPE    5  147
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  5
  YES                9                147

Clustering(66) Variable = 17p loss mutation analysis
D66V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   62  6
  17P LOSS WILD-TYPE 52  5
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                68                 57 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 6                  5 
$`17P LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       15.85        10.62        13.55        19.10        12.72        17.62 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3726 
       14.50         7.59         6.35         1.02         1.02         1.02 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3893 TCGA-AG-4007 TCGA-AG-4008 
        0.95         1.02         0.99         0.99         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-6644 TCGA-AH-6897 TCGA-BM-6198 
        1.94        40.96         0.49         0.72         4.60        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6155 
        6.02         6.94        13.97         7.99        11.01         7.36 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        6.97        19.99         0.26       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
      121.08        24.13        51.48         0.49         2.40         2.17 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 
        8.22         6.90         7.10         3.98         2.73         2.76 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 
        2.04         3.39         0.85         0.39         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6235 
        0.46        47.70 

$`17P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3583 
       19.53        11.77        10.39         8.45         7.33         2.01 
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-3999 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 
        1.02         1.02         0.99        20.94        13.02         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       10.98        49.94        38.93        61.94        38.01         1.45 
TCGA-AH-6643 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        0.69         1.81         6.02         9.37         4.70        60.00 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       10.98         9.99         5.03         8.98         6.97        27.91 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
        5.92         3.98         5.00        32.58         7.63         0.16 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 
        0.46         3.98         0.66         6.15         3.55         5.23 
TCGA-EI-6917 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
        7.79         2.17         1.02         0.66         0.53         1.08 
TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       18.25        47.08        20.91 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               0.16 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            121.08              61.94 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             7.035              5.230 
[1] "0.3 - 121.1 (7.0)" "0.2 - 61.9 (5.2)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        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-3581 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"17P LOSS WILD-TYPE"   "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        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-3581 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"17P LOSS WILD-TYPE"   "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        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-3581 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"17P LOSS WILD-TYPE"   "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     43   46
  17P LOSS WILD-TYPE   31   42
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               43                 31
  MALE                 46                 42
D66V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     79    6
  17P LOSS WILD-TYPE   64    7
                                clus
vv                               17P LOSS MUTATED 17P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        79                 64
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    2 15 62 10
  17P LOSS WILD-TYPE  7 14 47  4
D66V5, multiclass
                    vv
clus                 N0 N1 N2
  17P LOSS MUTATED   48 23 17
  17P LOSS WILD-TYPE 35 22 15
D66V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  17P LOSS MUTATED   67 14   0  7
  17P LOSS WILD-TYPE 56  8   2  6
D66V7, multiclass
                    vv
clus                  I II III IV
  17P LOSS MUTATED   14 33  25 14
  17P LOSS WILD-TYPE 16 17  25 11
D66V8, multiclass
D66V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   85
  17P LOSS WILD-TYPE    2   71
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                  2
  YES               85                 71

Clustering(67) Variable = 17q loss mutation analysis
D67V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    11   1
  17Q LOSS WILD-TYPE 103  10
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                113 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 10 
$`17Q LOSS MUTATED`
TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A02X TCGA-BM-6198 
        7.59         1.02        13.91        12.00        40.96        10.19 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6883 
        7.36         6.97        24.13         0.49         2.40         3.98 

$`17Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 
        7.33         1.02         2.01         1.02         0.99         1.02 
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-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-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-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-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.94        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-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-6156 TCGA-DC-6157 TCGA-DC-6160 
        9.99         5.03         8.98         6.97        27.91        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.92         3.98         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24       121.08        51.48        32.58         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
        7.10         6.15         3.55         2.73         5.23         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        2.76         2.04         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        47.70        47.08        20.91 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.49               0.16 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             40.96             121.08 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             7.475              6.020 
[1] "0.5 - 41.0 (7.5)"  "0.2 - 121.1 (6.0)"
        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 WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17Q LOSS WILD-TYPE" "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 WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17Q LOSS WILD-TYPE" "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 WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      6    9
  17Q LOSS WILD-TYPE   68   79
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                6                 68
  MALE                  9                 79
D67V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14    1
  17Q LOSS WILD-TYPE  129   12
                                clus
vv                               17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        14                129
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    0  4 10  1
  17Q LOSS WILD-TYPE  9 25 99 13
D67V5, multiclass
                    vv
clus                 N0 N1 N2
  17Q LOSS MUTATED    8  5  2
  17Q LOSS WILD-TYPE 75 40 30
D67V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  17Q LOSS MUTATED    11   2   0   1
  17Q LOSS WILD-TYPE 112  20   2  12
D67V7, multiclass
                    vv
clus                  I II III IV
  17Q LOSS MUTATED    3  5   5  2
  17Q LOSS WILD-TYPE 27 45  45 23
D67V8, multiclass
D67V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   13
  17Q LOSS WILD-TYPE    4  143
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 2                  4
  YES               13                143

Clustering(68) Variable = 18p loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   82  7
  18P LOSS WILD-TYPE 32  4
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                89                 36 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                  4 
$`18P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-3913 
       19.53        15.85        11.77        13.55        17.62        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       14.50         7.59         6.35         1.02         1.02         2.01 
TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3742 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3999 
        1.02         1.02         0.99         0.92         0.99         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-A016 TCGA-AG-A01J 
       25.94        23.01        17.03        15.91         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       12.00        12.00        70.03        10.98        51.98         1.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       40.96        38.01         0.49         0.69         0.72         4.60 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
       10.19         6.02         6.94         9.37        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        10.98        11.01         5.03         8.98         7.36 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
        6.97        27.91         6.97        19.99         5.92         5.00 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      119.51        41.33        57.24       121.08        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
        0.49         2.40         7.63         8.22         3.98         0.66 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        6.90         7.10         6.15         3.98         2.73         5.23 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        2.76         3.39         0.85         2.17         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.69         0.76         0.46        47.70 

$`18P LOSS WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3599 
       10.62        19.10        12.72         8.45         7.33         0.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
        0.95         1.02         0.99         1.02         0.99        20.94 
TCGA-AG-A015 TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 
       13.02        63.98        49.94        38.93        61.94         1.45 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6682 TCGA-DT-5265 
        1.81         6.02         4.70         9.99         3.98         0.26 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6882 TCGA-EI-6917 
       32.58         0.16         2.17         0.46         3.55         7.79 
TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        2.04         0.53         1.08        18.25        47.08        20.91 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.39               0.16 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            121.08              63.98 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              6.90               5.36 
[1] "0.4 - 121.1 (6.9)" "0.2 - 64.0 (5.4)" 
        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 WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P LOSS WILD-TYPE"   "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-3581 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        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 WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P LOSS WILD-TYPE"   "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-3581 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        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 WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P LOSS WILD-TYPE"   "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-3581 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "18P LOSS MUTATED"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D68V2, continuous
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     53   61
  18P LOSS WILD-TYPE   21   27
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               53                 21
  MALE                 61                 27
D68V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    107    5
  18P LOSS WILD-TYPE   36    8
                                clus
vv                               18P LOSS MUTATED 18P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       107                 36
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    2 19 82 11
  18P LOSS WILD-TYPE  7 10 27  3
D68V5, multiclass
                    vv
clus                 N0 N1 N2
  18P LOSS MUTATED   55 34 24
  18P LOSS WILD-TYPE 28 11  8
D68V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  18P LOSS MUTATED   86 18   2  7
  18P LOSS WILD-TYPE 37  4   0  6
D68V7, multiclass
                    vv
clus                  I II III IV
  18P LOSS MUTATED   18 36  37 18
  18P LOSS WILD-TYPE 12 14  13  7
D68V8, multiclass
D68V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4  110
  18P LOSS WILD-TYPE    2   46
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 4                  2
  YES              110                 46

Clustering(69) Variable = 18q loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   88  8
  18Q LOSS WILD-TYPE 26  3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                96                 29 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                  3 
$`18Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       19.53        15.85        11.77        13.55        19.10        17.62 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 
       10.39        14.50         7.59         6.35         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3887 
        2.01         1.02         1.02         0.95         0.99         0.92 
TCGA-AG-3893 TCGA-AG-3999 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-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-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-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       10.98        51.98         1.94        40.96        38.01         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72         4.60        10.19         6.02         6.94 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        60.00         7.99        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98         7.36         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       19.99         5.92         5.00       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      121.08        24.13        51.48         0.49         2.40         7.63 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
        2.17         8.22         3.98         0.66         6.90         7.10 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
        6.15         3.98         2.73         5.23         2.76         2.04 
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-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.76         0.46        47.70        47.08        20.91 

$`18Q LOSS WILD-TYPE`
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3599 TCGA-AG-3731 
       10.62        12.72         8.45         7.33         0.99         1.02 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 
        0.99         1.02         0.99        20.94        13.02        49.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6624 
       38.93        61.94         1.45         1.81         6.02         4.70 
TCGA-DC-5337 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 
        9.99         3.98         0.26        32.58         0.16         0.46 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 
        3.55         7.79         0.53         1.08        18.25 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.39               0.16 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            121.08              61.94 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              6.92               4.70 
[1] "0.4 - 121.1 (6.9)" "0.2 - 61.9 (4.7)" 
        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 WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q LOSS WILD-TYPE"   "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-3581 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "18Q LOSS MUTATED"   "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 WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q LOSS WILD-TYPE"   "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-3581 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "18Q LOSS MUTATED"   "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 WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q LOSS WILD-TYPE"   "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-3581 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-G5-6572         TCGA-G5-6641 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
[1] "hr=" "1.7"
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     60   66
  18Q LOSS WILD-TYPE   14   22
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               60                 14
  MALE                 66                 22
D69V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    113    9
  18Q LOSS WILD-TYPE   30    4
                                clus
vv                               18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       113                 30
  RECTAL MUCINOUS ADENOCARCINOMA                9                  4
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    3 20 90 12
  18Q LOSS WILD-TYPE  6  9 19  2
D69V5, multiclass
                    vv
clus                 N0 N1 N2
  18Q LOSS MUTATED   61 37 26
  18Q LOSS WILD-TYPE 22  8  6
D69V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  18Q LOSS MUTATED   94 19   2  9
  18Q LOSS WILD-TYPE 29  3   0  4
D69V7, multiclass
                    vv
clus                  I II III IV
  18Q LOSS MUTATED   19 41  40 20
  18Q LOSS WILD-TYPE 11  9  10  5
D69V8, multiclass
D69V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  122
  18Q LOSS WILD-TYPE    2   34
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 4                  2
  YES              122                 34

Clustering(70) Variable = 19p loss mutation analysis
D70V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED     3   2
  19P LOSS WILD-TYPE 111   9
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                120 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                  9 
$`19P LOSS MUTATED`
TCGA-DC-6155 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6513 
        7.36        24.13        51.48         0.49         6.90 

$`19P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-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-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-6156 TCGA-DC-6157 TCGA-DC-6158 
        9.99         5.03         8.98         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.92         3.98         5.00         0.26       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       41.33        57.24       121.08        32.58         2.40         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        0.16         2.17         8.22         0.46         3.98         0.66 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        7.10         6.15         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        7.79         2.76         2.04         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        47.70        47.08        20.91 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.49               0.16 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             51.48             121.08 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             7.360              6.085 
[1] "0.5 - 51.5 (7.4)"  "0.2 - 121.1 (6.1)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P LOSS WILD-TYPE" "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 WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P LOSS WILD-TYPE" "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 WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P LOSS WILD-TYPE" "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 WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "3.7"
D70V2, continuous
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4    3
  19P LOSS WILD-TYPE   70   85
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 70
  MALE                  3                 85
D70V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6    0
  19P LOSS WILD-TYPE  137   13
                                clus
vv                               19P LOSS MUTATED 19P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                137
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED     0   1   5   1
  19P LOSS WILD-TYPE   9  28 104  13
D70V5, multiclass
                    vv
clus                 N0 N1 N2
  19P LOSS MUTATED    3  3  1
  19P LOSS WILD-TYPE 80 42 31
D70V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  19P LOSS MUTATED     6   1   0   0
  19P LOSS WILD-TYPE 117  21   2  13
D70V7, multiclass
                    vv
clus                  I II III IV
  19P LOSS MUTATED    0  3   3  1
  19P LOSS WILD-TYPE 30 47  47 24
D70V8, multiclass
D70V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    7
  19P LOSS WILD-TYPE    6  149
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 0                  6
  YES                7                149

Clustering(71) Variable = 19q loss mutation analysis
D71V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED     4   1
  19Q LOSS WILD-TYPE 110  10
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                120 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 10 
$`19Q LOSS MUTATED`
TCGA-AG-A011 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 
       17.03        24.13         0.49         6.90         3.98 

$`19Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39        14.50         8.45         7.59 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
        6.35         7.33         1.02         1.02         2.01         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         1.02         0.95         1.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 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-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.94        23.01        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         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98         7.36         6.97        27.91         6.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.92         3.98         5.00         0.26       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       41.33        57.24       121.08        51.48        32.58         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        7.63         0.16         2.17         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
        0.66         7.10         6.15         3.55         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        7.79         2.76         2.04         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        47.70        47.08        20.91 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.16 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             24.13             121.08 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              6.90               6.25 
[1] "0.5 - 24.1 (6.9)"  "0.2 - 121.1 (6.2)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q LOSS WILD-TYPE" "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 WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q LOSS WILD-TYPE" "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 WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q LOSS WILD-TYPE" "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 WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr=" "7.2"
D71V2, continuous
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    4
  19Q LOSS WILD-TYPE   71   84
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 71
  MALE                  4                 84
D71V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      6    0
  19Q LOSS WILD-TYPE  137   13
                                clus
vv                               19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                137
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED     0   0   6   1
  19Q LOSS WILD-TYPE   9  29 103  13
D71V5, multiclass
                    vv
clus                 N0 N1 N2
  19Q LOSS MUTATED    5  1  1
  19Q LOSS WILD-TYPE 78 44 31
D71V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  19Q LOSS MUTATED     7   0   0   0
  19Q LOSS WILD-TYPE 116  22   2  13
D71V7, multiclass
                    vv
clus                  I II III IV
  19Q LOSS MUTATED    0  5   2  0
  19Q LOSS WILD-TYPE 30 45  48 25
D71V8, multiclass
D71V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    7
  19Q LOSS WILD-TYPE    6  149
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 0                  6
  YES                7                149

Clustering(72) Variable = 20p loss mutation analysis
D72V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    11   2
  20P LOSS WILD-TYPE 103   9
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                13                112 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                  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-6683 TCGA-EI-6881 
       70.03        63.98         1.94        38.93         5.00         6.15 
TCGA-F5-6702 
        2.17 

$`20P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       19.53        15.85        11.77        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        17.62        10.39         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.94         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       15.91        13.02         1.02        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-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         9.99         5.03         8.98         7.36 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        6.97        27.91         6.97        19.99         5.92         3.98 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        0.26       119.51        41.33        57.24       121.08        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         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.17         8.22         0.46         3.98         0.66         6.90 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
        7.10         3.55         3.98         2.73         5.23         7.79 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        2.76         2.04         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        47.70        47.08        20.91 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.99               0.16 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             70.03             121.08 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            12.000              6.185 
[1] "1.0 - 70.0 (12.0)" "0.2 - 121.1 (6.2)"
        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-3581 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "20P LOSS MUTATED"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        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-3581 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "20P LOSS MUTATED"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        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-3581 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3599         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-3887         TCGA-AG-3892         TCGA-AG-3893 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
  "20P LOSS MUTATED"   "20P LOSS MUTATED"   "20P LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
  "20P LOSS MUTATED"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D72V2, continuous
D72V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9    9
  20P LOSS WILD-TYPE   65   79
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                9                 65
  MALE                  9                 79
D72V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     15    2
  20P LOSS WILD-TYPE  128   11
                                clus
vv                               20P LOSS MUTATED 20P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        15                128
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    0  3 13  2
  20P LOSS WILD-TYPE  9 26 96 12
D72V5, multiclass
                    vv
clus                 N0 N1 N2
  20P LOSS MUTATED   10  5  3
  20P LOSS WILD-TYPE 73 40 29
D72V6, multiclass
                    vv
clus                  M0  M1 M1A  MX
  20P LOSS MUTATED    14   3   0   1
  20P LOSS WILD-TYPE 109  19   2  12
D72V7, multiclass
                    vv
clus                  I II III IV
  20P LOSS MUTATED    1  8   5  4
  20P LOSS WILD-TYPE 29 42  45 21
D72V8, multiclass
D72V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   18
  20P LOSS WILD-TYPE    6  138
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  6
  YES               18                138

Clustering(73) Variable = 21q loss mutation analysis
D73V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   29  3
  21Q LOSS WILD-TYPE 85  8
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                32                 93 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                  8 
$`21Q LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       15.85        11.77        14.50         7.59         6.35         7.33 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
        1.02         1.02         0.99        12.00        12.00        63.98 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6643 TCGA-CL-4957 TCGA-DC-6155 
       10.98        61.94        40.96         0.69        13.97         7.36 
TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
        6.97       119.51        57.24       121.08        51.48        32.58 
TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-7002 TCGA-EI-7004 
        2.17         3.98         0.66         6.90         2.76         2.04 
TCGA-F5-6810 TCGA-F5-6863 
        0.39         0.76 

$`21Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       19.53        10.62        13.55        19.10        12.72        17.62 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3726 TCGA-AG-3727 
       10.39         8.45         1.02         2.01         1.02         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-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-A01W TCGA-AG-A023 
       15.91        13.02         1.02         1.02        70.03        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.94         1.94        38.93        38.01         0.49         1.45 
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-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.94         9.37         4.70        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         9.99         5.03         8.98         6.97        27.91 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.92         3.98         5.00         0.26        41.33 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       24.13         0.49         2.40         7.63         0.16         8.22 
TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        0.46         7.10         6.15         3.55         3.98         2.73 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        5.23         7.79         3.39         0.85         2.17         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         0.53         1.08         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       47.70        47.08        20.91 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.39               0.16 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            121.08              70.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             7.475              5.920 
[1] "0.4 - 121.1 (7.5)" "0.2 - 70.0 (5.9)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q LOSS WILD-TYPE"   "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-3581 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
  "21Q LOSS MUTATED" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q LOSS WILD-TYPE"   "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-3581 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
  "21Q LOSS MUTATED" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q LOSS WILD-TYPE"   "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-3581 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
  "21Q LOSS MUTATED" "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-3887         TCGA-AG-3892         TCGA-AG-3893 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D73V2, continuous
D73V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     22   21
  21Q LOSS WILD-TYPE   52   67
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               22                 52
  MALE                 21                 67
D73V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     38    2
  21Q LOSS WILD-TYPE  105   11
                                clus
vv                               21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        38                105
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    0  9 30  4
  21Q LOSS WILD-TYPE  9 20 79 10
D73V5, multiclass
                    vv
clus                 N0 N1 N2
  21Q LOSS MUTATED   16 17 10
  21Q LOSS WILD-TYPE 67 28 22
D73V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  21Q LOSS MUTATED   34  6   0  3
  21Q LOSS WILD-TYPE 89 16   2 10
D73V7, multiclass
                    vv
clus                  I II III IV
  21Q LOSS MUTATED    5 10  18  8
  21Q LOSS WILD-TYPE 25 40  32 17
D73V8, multiclass
D73V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   41
  21Q LOSS WILD-TYPE    4  115
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 2                  4
  YES               41                115

Clustering(74) Variable = 22q loss mutation analysis
D74V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   23  4
  22Q LOSS WILD-TYPE 91  7
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                27                 98 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                  7 
$`22Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3999 
       13.55         7.59         7.33         1.02         2.01         1.02 
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-CL-4957 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       10.19        13.97         7.36         6.97        19.99         3.98 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6881 TCGA-F5-6810 
        5.00        41.33        51.48         2.40         6.15         0.39 
TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6641 
        0.66         0.76        20.91 

$`22Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       19.53        15.85        11.77        10.62        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3582 
       17.62        10.39        14.50         8.45         6.35         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        1.02         0.99         1.02         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 
        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-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-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        70.03        63.98        51.98        49.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.94        40.96        38.01         1.45         0.69         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81         6.02         6.02         6.94         9.37         4.70 
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         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
        8.98         6.97        27.91         5.92         0.26       119.51 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24       121.08        24.13        32.58         0.49         7.63 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        0.16         2.17         8.22         0.46         3.98         0.66 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        6.90         7.10         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        7.79         2.76         2.04         3.39         0.85         2.17 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.69         0.53         1.08         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 
       47.70        47.08 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.39               0.16 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             51.48             121.08 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             6.970              6.185 
[1] "0.4 - 51.5 (7.0)"  "0.2 - 121.1 (6.2)"
        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 WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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 WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"22Q LOSS WILD-TYPE"   "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 WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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 WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"22Q LOSS WILD-TYPE"   "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 WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3581 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3599         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 WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3892         TCGA-AG-3893 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3999         TCGA-AG-4001 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4022 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01J         TCGA-AG-A01L         TCGA-AG-A01N 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A023         TCGA-AG-A025         TCGA-AG-A026 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A032         TCGA-AH-6544         TCGA-AH-6547 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-AH-6897 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6903         TCGA-BM-6198         TCGA-CI-6619 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6622         TCGA-CI-6623 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-4957         TCGA-CL-5917 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-4745         TCGA-DC-4749 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6154 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6156         TCGA-DC-6157 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A0XA         TCGA-DY-A1DC         TCGA-DY-A1DD 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DE         TCGA-DY-A1DF         TCGA-DY-A1DG 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EF-5831 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6509         TCGA-EI-6510         TCGA-EI-6511 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6512         TCGA-EI-6513         TCGA-EI-6514 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6881         TCGA-EI-6882         TCGA-EI-6883 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6884         TCGA-EI-6885         TCGA-EI-6917 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7002         TCGA-EI-7004         TCGA-F5-6465 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
[1] "hr=" "4.2"
D74V2, continuous
D74V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     17   25
  22Q LOSS WILD-TYPE   57   63
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               17                 57
  MALE                 25                 63
D74V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     37    4
  22Q LOSS WILD-TYPE  106    9
                                clus
vv                               22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        37                106
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    1  6 32  3
  22Q LOSS WILD-TYPE  8 23 77 11
D74V5, multiclass
                    vv
clus                 N0 N1 N2
  22Q LOSS MUTATED   17 17  7
  22Q LOSS WILD-TYPE 66 28 25
D74V6, multiclass
                    vv
clus                 M0 M1 M1A MX
  22Q LOSS MUTATED   30  6   0  5
  22Q LOSS WILD-TYPE 93 16   2  8
D74V7, multiclass
                    vv
clus                  I II III IV
  22Q LOSS MUTATED    4 13  17  6
  22Q LOSS WILD-TYPE 26 37  33 19
D74V8, multiclass
D74V9, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   39
  22Q LOSS WILD-TYPE    3  117
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                  3
  YES               39                117

Clustering(75) Variable = Xq loss mutation analysis
D75V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED     3   0
  XQ LOSS WILD-TYPE 111  11
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               122 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                0                11 
$`XQ LOSS MUTATED`
TCGA-AF-2693 TCGA-AG-A00Y TCGA-AG-A02X 
       19.10        23.01        40.96 

$`XQ LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       19.53        15.85        11.77        10.62        13.55        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       17.62        10.39        14.50         8.45         7.59         6.35 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         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-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-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.93        61.94        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         9.99         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.36         6.97        27.91         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        3.98         5.00         0.26       119.51        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      121.08        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 
        7.63         0.16         2.17         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        0.66         6.90         7.10         6.15         3.55         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        2.73         5.23         7.79         2.76         2.04         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        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            19.10              0.16 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            40.96            121.08 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           23.010             6.085 
[1] "19.1 - 41.0 (23.0)" "0.2 - 121.1 (6.1)" 
       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-3581        TCGA-AG-3582 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6641 
"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-3581        TCGA-AG-3582 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3583        TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878 
"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-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6641 
"XQ LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D75V2, continuous
D75V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    4
  XQ LOSS WILD-TYPE   72   84
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2                72
  MALE                 4                84
D75V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      5    0
  XQ LOSS WILD-TYPE  138   13
                                clus
vv                               XQ LOSS MUTATED XQ LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               138
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED     0   2   4   0
  XQ LOSS WILD-TYPE   9  27 105  14
D75V5, multiclass
                   vv
clus                N0 N1 N2
  XQ LOSS MUTATED    4  0  2
  XQ LOSS WILD-TYPE 79 45 30
D75V6, multiclass
                   vv
clus                 M0  M1 M1A  MX
  XQ LOSS MUTATED     3   2   0   1
  XQ LOSS WILD-TYPE 120  20   2  12
D75V7, multiclass
                   vv
clus                 I II III IV
  XQ LOSS MUTATED    2  2   0  2
  XQ LOSS WILD-TYPE 28 48  50 23
D75V8, multiclass
D75V9, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    6
  XQ LOSS WILD-TYPE    6  150
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                0                 6
  YES               6               150
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
                     "HISTOLOGICAL.TYPE" 
                                      V5 
                           "PATHOLOGY.T" 
                                      V6 
                           "PATHOLOGY.N" 
                                      V7 
                   "PATHOLOGICSPREAD(M)" 
                                      V8 
                           "TUMOR.STAGE" 
                                      V9 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
> q(save="no")
